[ { "id": "P38886-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "P38886-1", "length": 268, "uniprot_id": "RPN10_YEAST", "protein_name": "26S proteasome regulatory subunit RPN10", "refseq_ac": "NP_012070", "refseq_name": "proteasome regulatory particle base subunit RPN10", "gene_name": "RPN10", "gene_names_uniprotkb": "RPN10; MCB1; SUN1", "gene_names_refseq": "MCB1; RPN10; SUN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38886", "url": "https://www.uniprot.org/uniprotkb/P38886" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001243", "url": "https://www.yeastgenome.org/locus/S000001243", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQQRQERLRQQQQQQDQPEQ", "down_seq": "EQPEQHQDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000001243", "url": "https://www.yeastgenome.org/locus/S000001243" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser259" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "43", "end_pos": "43" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38886-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P38886-1", "length": 268, "uniprot_id": "RPN10_YEAST", "protein_name": "26S proteasome regulatory subunit RPN10", "refseq_ac": "NP_012070", "refseq_name": "proteasome regulatory particle base subunit RPN10", "gene_name": "RPN10", "gene_names_uniprotkb": "RPN10; MCB1; SUN1", "gene_names_refseq": "MCB1; RPN10; SUN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38886", "url": "https://www.uniprot.org/uniprotkb/P38886" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001243", "url": "https://www.yeastgenome.org/locus/S000001243", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RTRFEAQIDSVEFIFQAKRN", "down_seq": "NPENTVGLISGAGANPRVLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001243", "url": "https://www.yeastgenome.org/locus/S000001243" }, { "database": "iPTMnet", "id": "P38886", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38886" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser43" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "43", "end_pos": "43" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38932-1.572.572", "start_pos": 572, "end_pos": 572, "uniprot_canonical_ac": "P38932-1", "length": 577, "uniprot_id": "VPS45_YEAST", "protein_name": "Vacuolar protein sorting-associated protein 45", "refseq_ac": "NP_011420", "refseq_name": "Vps45p", "gene_name": "VPS45", "gene_names_uniprotkb": "VPS45; STT10; VPL28", "gene_names_refseq": "STT10; VPL28; VPS45", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38932", "url": "https://www.uniprot.org/uniprotkb/P38932" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "iPTMnet", "id": "P38932", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38932" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P38932", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38932", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NRMRVVLGGTSILSTKEYMD", "down_seq": "IRSAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P38932", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38932" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Ser572" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "572", "end_pos": "572" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38960-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P38960-1", "length": 494, "uniprot_id": "STN1_YEAST", "protein_name": "Protein STN1", "refseq_ac": "NP_010367", "refseq_name": "Stn1p", "gene_name": "STN1", "gene_names_uniprotkb": "STN1; D4456; YD8554.15", "gene_names_refseq": "STN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres.", "journal": "Genes & development", "date": "2009-12-15", "authors": "Sun Jia, Yu Eun Young, Yang Yuting, Confer Laura A, Sun Steven H, Wan Ke, Lue Neal F, Lei Ming", "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "reference": [ { "type": "PubMed", "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938" } ] } ], "crossref": [ { "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VNRLVSQGLIGLKDKTSETF", "down_seq": "LLPLKNLFEYAEKRISVLMK", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Modest telomere elongation phenotype.", "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" }, { "database": "PubMed", "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "397", "end_pos": "397" }, { "start_pos": "466", "end_pos": "466" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "223", "end_pos": "223" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "283", "end_pos": "283" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38960-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "P38960-1", "length": 494, "uniprot_id": "STN1_YEAST", "protein_name": "Protein STN1", "refseq_ac": "NP_010367", "refseq_name": "Stn1p", "gene_name": "STN1", "gene_names_uniprotkb": "STN1; D4456; YD8554.15", "gene_names_refseq": "STN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Stn1-Ten1 is an Rpa2-Rpa3-like complex at telomeres.", "journal": "Genes & development", "date": "2009-12-15", "authors": "Sun Jia, Yu Eun Young, Yang Yuting, Confer Laura A, Sun Steven H, Wan Ke, Lue Neal F, Lei Ming", "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "reference": [ { "type": "PubMed", "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938" } ] } ], "crossref": [ { "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "DVFKECLKRTKKQYPEVLKN", "down_seq": "WIDLDPKNGMEDQNSGILLH", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "E", "comment": "Elongated telomeres.", "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" }, { "database": "PubMed", "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938" } ] }, { "sequence_org": "W", "sequence_mut": "R", "comment": "Elongated telomeres and severe growth defects.", "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" }, { "database": "PubMed", "id": "20008938", "url": "https://glygen.org/publication/PubMed/20008938" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "397", "end_pos": "397" }, { "start_pos": "466", "end_pos": "466" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "223", "end_pos": "223" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "283", "end_pos": "283" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38960-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "P38960-1", "length": 494, "uniprot_id": "STN1_YEAST", "protein_name": "Protein STN1", "refseq_ac": "NP_010367", "refseq_name": "Stn1p", "gene_name": "STN1", "gene_names_uniprotkb": "STN1; D4456; YD8554.15", "gene_names_refseq": "STN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cdk1 regulates the temporal recruitment of telomerase and Cdc13-Stn1-Ten1 complex for telomere replication.", "journal": "Molecular and cellular biology", "date": "2014-01", "authors": "Liu Chang-Ching, Gopalakrishnan Veena, Poon Lai-Fong, Yan TingDong, Li Shang", "evidence": [ { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" } ], "reference": [ { "type": "PubMed", "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896" } ] } ], "crossref": [ { "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002489", "url": "https://www.yeastgenome.org/locus/S000002489", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TPETSQIEVVNPDFVGIGYK", "down_seq": "PESKRNETTFIEQLQEERLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" }, { "database": "PubMed", "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896" } ], "site_lbl": "Thr223" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002489", "url": "https://www.yeastgenome.org/locus/S000002489" }, { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" }, { "database": "PubMed", "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896" } ], "site_lbl": "Thr223" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "397", "end_pos": "397" }, { "start_pos": "466", "end_pos": "466" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "223", "end_pos": "223" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "283", "end_pos": "283" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38960-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P38960-1", "length": 494, "uniprot_id": "STN1_YEAST", "protein_name": "Protein STN1", "refseq_ac": "NP_010367", "refseq_name": "Stn1p", "gene_name": "STN1", "gene_names_uniprotkb": "STN1; D4456; YD8554.15", "gene_names_refseq": "STN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cdk1 regulates the temporal recruitment of telomerase and Cdc13-Stn1-Ten1 complex for telomere replication.", "journal": "Molecular and cellular biology", "date": "2014-01", "authors": "Liu Chang-Ching, Gopalakrishnan Veena, Poon Lai-Fong, Yan TingDong, Li Shang", "evidence": [ { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" } ], "reference": [ { "type": "PubMed", "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896" } ] } ], "crossref": [ { "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002489", "url": "https://www.yeastgenome.org/locus/S000002489", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETTFIEQLQEERLKDELEII", "down_seq": "PYNSTDTSNSVHSLSFRFVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" }, { "database": "PubMed", "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896" } ], "site_lbl": "Ser250" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002489", "url": "https://www.yeastgenome.org/locus/S000002489" }, { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" }, { "database": "PubMed", "id": "24164896", "url": "https://glygen.org/publication/PubMed/24164896" } ], "site_lbl": "Ser250" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "397", "end_pos": "397" }, { "start_pos": "466", "end_pos": "466" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "223", "end_pos": "223" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "283", "end_pos": "283" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38960-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P38960-1", "length": 494, "uniprot_id": "STN1_YEAST", "protein_name": "Protein STN1", "refseq_ac": "NP_010367", "refseq_name": "Stn1p", "gene_name": "STN1", "gene_names_uniprotkb": "STN1; D4456; YD8554.15", "gene_names_refseq": "STN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38960", "url": "https://www.uniprot.org/uniprotkb/P38960" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002489", "url": "https://www.yeastgenome.org/locus/S000002489", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLSFRFVSSLKDFPETHFLN", "down_seq": "GDQIDNGNDEQLKKLEYQSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P38960", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38960" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000002489", "url": "https://www.yeastgenome.org/locus/S000002489" } ], "site_lbl": "Ser283" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "397", "end_pos": "397" }, { "start_pos": "466", "end_pos": "466" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "223", "end_pos": "223" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "283", "end_pos": "283" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.1085.1085", "start_pos": 1085, "end_pos": 1085, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGLEVKVKLGNIWKESLIEL", "down_seq": "GGQRSLIALSLIMALLQFRP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" } ], "site_lbl": "Ser1085" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HKEGTISKLENKENGLLNEI", "down_seq": "RLKTSLSIKVENLNDTTEKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" }, { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser313" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P38989-1.317.317", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P38989-1.318.318", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TISKLENKENGLLNEISRLK", "down_seq": "SLSIKVENLNDTTEKSKALE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" }, { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr317" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P38989-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P38989-1.318.318", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ISKLENKENGLLNEISRLKT", "down_seq": "LSIKVENLNDTTEKSKALES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" }, { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser318" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P38989-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P38989-1.317.317", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.719.719", "start_pos": 719, "end_pos": 719, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HVTEELQTQYATSQKTKTIQ", "down_seq": "DLNLSLHKLDLAKRNLDANP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" }, { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser719" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P38989-1.724.724", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.724.724", "start_pos": 724, "end_pos": 724, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQTQYATSQKTKTIQSDLNL", "down_seq": "LHKLDLAKRNLDANPSSQII", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" }, { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser724" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P38989-1.719.719", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P38989-1.812.812", "start_pos": 812, "end_pos": 812, "uniprot_canonical_ac": "P38989-1", "length": 1170, "uniprot_id": "SMC2_YEAST", "protein_name": "Structural maintenance of chromosomes protein 2", "refseq_ac": "NP_116687", "refseq_name": "condensin subunit SMC2", "gene_name": "SMC2", "gene_names_uniprotkb": "SMC2", "gene_names_refseq": "SMC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P38989", "url": "https://www.uniprot.org/uniprotkb/P38989" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLNELKKELKLLAKELEEQE", "down_seq": "ESERKYDLFQNLELETEQLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001927", "url": "https://www.yeastgenome.org/locus/S000001927" }, { "database": "iPTMnet", "id": "P38989", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P38989" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser812" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "719", "end_pos": "719" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "812", "end_pos": "812" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39013-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P39013-1", "length": 349, "uniprot_id": "END3_YEAST", "protein_name": "Actin cytoskeleton-regulatory complex protein END3", "refseq_ac": "NP_014315", "refseq_name": "End3p", "gene_name": "END3", "gene_names_uniprotkb": "END3; N2307", "gene_names_refseq": "END3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEIPASLPNSLAEVCNKKQL", "down_seq": "YDLRSSQPPTKRKEEANEVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser225" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "225", "end_pos": "225" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "278", "end_pos": "278" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39013-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "P39013-1", "length": 349, "uniprot_id": "END3_YEAST", "protein_name": "Actin cytoskeleton-regulatory complex protein END3", "refseq_ac": "NP_014315", "refseq_name": "End3p", "gene_name": "END3", "gene_names_uniprotkb": "END3; N2307", "gene_names_refseq": "END3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DNGQNSSSDSSGSNVLSNED", "down_seq": "IKQKYASLTDDQVANMREQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser269" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "225", "end_pos": "225" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "278", "end_pos": "278" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P39013-1.274.274", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39013-1.276.276", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39013-1.278.278", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39013-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P39013-1", "length": 349, "uniprot_id": "END3_YEAST", "protein_name": "Actin cytoskeleton-regulatory complex protein END3", "refseq_ac": "NP_014315", "refseq_name": "End3p", "gene_name": "END3", "gene_names_uniprotkb": "END3; N2307", "gene_names_refseq": "END3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SSSDSSGSNVLSNEDSIKQK", "down_seq": "ASLTDDQVANMREQLEGLLN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Tyr274" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "225", "end_pos": "225" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "278", "end_pos": "278" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P39013-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39013-1.276.276", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39013-1.278.278", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39013-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "P39013-1", "length": 349, "uniprot_id": "END3_YEAST", "protein_name": "Actin cytoskeleton-regulatory complex protein END3", "refseq_ac": "NP_014315", "refseq_name": "End3p", "gene_name": "END3", "gene_names_uniprotkb": "END3; N2307", "gene_names_refseq": "END3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SDSSGSNVLSNEDSIKQKYA", "down_seq": "LTDDQVANMREQLEGLLNYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser276" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "225", "end_pos": "225" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "278", "end_pos": "278" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P39013-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39013-1.274.274", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39013-1.278.278", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39013-1.278.278", "start_pos": 278, "end_pos": 278, "uniprot_canonical_ac": "P39013-1", "length": 349, "uniprot_id": "END3_YEAST", "protein_name": "Actin cytoskeleton-regulatory complex protein END3", "refseq_ac": "NP_014315", "refseq_name": "End3p", "gene_name": "END3", "gene_names_uniprotkb": "END3; N2307", "gene_names_refseq": "END3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39013", "url": "https://www.uniprot.org/uniprotkb/P39013" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSGSNVLSNEDSIKQKYASL", "down_seq": "DDQVANMREQLEGLLNYKKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005028", "url": "https://www.yeastgenome.org/locus/S000005028" }, { "database": "iPTMnet", "id": "P39013", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39013" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr278" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "225", "end_pos": "225" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "278", "end_pos": "278" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39013-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39013-1.274.274", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39013-1.276.276", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The amino-terminal portion of the F-box protein Met30p mediates its nuclear import and assimilation into an SCF complex.", "journal": "The Journal of biological chemistry", "date": "2004-02-20", "authors": "Brunson Lee Ellen, Dixon Cheryl, Kozubowski Lukasz, Mathias Neal", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "reference": [ { "type": "PubMed", "id": "14660673", "url": "https://glygen.org/publication/PubMed/14660673" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "14660673", "url": "https://glygen.org/publication/PubMed/14660673", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QLSYISSLVTHMIKIDFISI", "down_seq": "PQELSLKILSYLDCQSLCNA", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Strongly reduces nuclear localization; inhibits interaction with SKP1/CBF3D.", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "14660673", "url": "https://glygen.org/publication/PubMed/14660673" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P39014-1.190.190", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The amino-terminal portion of the F-box protein Met30p mediates its nuclear import and assimilation into an SCF complex.", "journal": "The Journal of biological chemistry", "date": "2004-02-20", "authors": "Brunson Lee Ellen, Dixon Cheryl, Kozubowski Lukasz, Mathias Neal", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "reference": [ { "type": "PubMed", "id": "14660673", "url": "https://glygen.org/publication/PubMed/14660673" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "14660673", "url": "https://glygen.org/publication/PubMed/14660673", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YISSLVTHMIKIDFISILPQ", "down_seq": "LSLKILSYLDCQSLCNATRV", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Strongly reduces nuclear localization; inhibits interaction with SKP1/CBF3D.", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "14660673", "url": "https://glygen.org/publication/PubMed/14660673" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39014-1.187.187", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of residues in the WD-40 repeat motif of the F-box protein Met30p required for interaction with its substrate Met4p.", "journal": "Molecular genetics and genomics : MGG", "date": "2005-06", "authors": "Brunson Lee Ellen, Dixon Cheryl, LeFebvre Aaron, Sun Lisa, Mathias Neal", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "reference": [ { "type": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VWNYITGECISTYRGHSDSV", "down_seq": "SVDSYQKVIVSGSADKTVKV", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Inactivates MET30 and prevents MET4 interaction; when associated with A-425 and A-467.", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.425.425", "start_pos": 425, "end_pos": 425, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of residues in the WD-40 repeat motif of the F-box protein Met30p required for interaction with its substrate Met4p.", "journal": "Molecular genetics and genomics : MGG", "date": "2005-06", "authors": "Brunson Lee Ellen, Dixon Cheryl, LeFebvre Aaron, Sun Lisa, Mathias Neal", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "reference": [ { "type": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KVWHVESRTCYTLRGHTEWV", "down_seq": "CVKLHPKSFSCFSCSDDTTI", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Inactivates MET30 and prevents MET4 interaction; when associated with D-530 or D-386 and A-467.", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.467.467", "start_pos": 467, "end_pos": 467, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of residues in the WD-40 repeat motif of the F-box protein Met30p required for interaction with its substrate Met4p.", "journal": "Molecular genetics and genomics : MGG", "date": "2005-06", "authors": "Brunson Lee Ellen, Dixon Cheryl, LeFebvre Aaron, Sun Lisa, Mathias Neal", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "reference": [ { "type": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MWDIRTNSCLKVFRGHVGQV", "down_seq": "KIIPLTIKDVENLATDNTSD", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Inactivates MET30 and prevents MET4 interaction; when associated with D-386 and A-425.", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.530.530", "start_pos": 530, "end_pos": 530, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of residues in the WD-40 repeat motif of the F-box protein Met30p required for interaction with its substrate Met4p.", "journal": "Molecular genetics and genomics : MGG", "date": "2005-06", "authors": "Brunson Lee Ellen, Dixon Cheryl, LeFebvre Aaron, Sun Lisa, Mathias Neal", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "reference": [ { "type": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "EQETVLDENIPYPTHLLSCG", "down_seq": "DNTIKLWDVKTGKCIRTQFG", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Inactivates MET30 and prevents MET4 interaction; when associated with A-425.", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "15883825", "url": "https://glygen.org/publication/PubMed/15883825" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae.", "journal": "Molecular biology of the cell", "date": "2014-05", "authors": "Sadhu Meru J, Moresco James J, Zimmer Anjali D, Yates John R, Rine Jasper", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLPEYNFTKFCYRHNPDIQF", "down_seq": "PTHTACYKQDLKRTQEINAN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser105" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P39014-1.107.107", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PEYNFTKFCYRHNPDIQFSP", "down_seq": "HTACYKQDLKRTQEINANIA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr107" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39014-1.105.105", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NWRKGHCRIQEFKGHMDGVL", "down_seq": "LQFNYRLLFTGSYDSTIGIW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr307" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NNSSEMTDTAMMPPLKRLLI", "down_seq": "GSSDDLAQGSSGKKKMTMAT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr45" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P39014-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39014-1.48.48", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae.", "journal": "Molecular biology of the cell", "date": "2014-05", "authors": "Sadhu Meru J, Moresco James J, Zimmer Anjali D, Yates John R, Rine Jasper", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSEMTDTAMMPPLKRLLITG", "down_seq": "SDDLAQGSSGKKKMTMATRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser47" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39014-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39014-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39014-1.67.67", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEMTDTAMMPPLKRLLITGS", "down_seq": "DDLAQGSSGKKKMTMATRSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser48" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39014-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39014-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39014-1.67.67", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSDDLAQGSSGKKKMTMATR", "down_seq": "PSSSPDLATNDSGTRVQPLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser67" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39014-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P39014-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39014-1.69.69", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39014-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39014-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DDLAQGSSGKKKMTMATRSP", "down_seq": "SSPDLATNDSGTRVQPLPEY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser69" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39014-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39014-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39014-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Multiple inputs control sulfur-containing amino acid synthesis in Saccharomyces cerevisiae.", "journal": "Molecular biology of the cell", "date": "2014-05", "authors": "Sadhu Meru J, Moresco James J, Zimmer Anjali D, Yates John R, Rine Jasper", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLAQGSSGKKKMTMATRSPS", "down_seq": "SPDLATNDSGTRVQPLPEYN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "24648496", "url": "https://glygen.org/publication/PubMed/24648496" }, { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser70" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39014-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39014-1.69.69", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39014-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39014-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "P39014-1", "length": 640, "uniprot_id": "MET30_YEAST", "protein_name": "F-box protein MET30", "refseq_ac": "NP_012218", "refseq_name": "ubiquitin-binding SDF ubiquitin ligase complex subunit MET30", "gene_name": "MET30", "gene_names_uniprotkb": "MET30", "gene_names_refseq": "MET30; ZRG11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39014", "url": "https://www.uniprot.org/uniprotkb/P39014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAQGSSGKKKMTMATRSPSS", "down_seq": "PDLATNDSGTRVQPLPEYNF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001308", "url": "https://www.yeastgenome.org/locus/S000001308" }, { "database": "iPTMnet", "id": "P39014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39014" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser71" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "467", "end_pos": "467" }, { "start_pos": "530", "end_pos": "530" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39014-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39014-1.69.69", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39014-1.70.70", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.41.55", "start_pos": 41, "end_pos": 55, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "SADPSKARKNRPRPS", "start_aa": "S", "up_seq": "PPKEIVKSNTSSKKADVPPP", "down_seq": "GNEGAIRDKTAGRRNNRSKD", "mutagenesis": [ { "sequence_org": "SADPSKARKNRPRPS", "sequence_mut": "AADPAKARKNRPRPA", "comment": "Decreased phosphorylation by mTOR/TOR1, leading to reduced ribosome reactivation in response to nutrient replenishment.", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] }, { "sequence_org": "SADPSKARKNRPRPS", "sequence_mut": "EADPEKARKNRPRPE", "comment": "Mimics phosphorylation by mTOR/TOR1, leading to decreased ability to mediate ribosome hibernation.", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39015-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39015-1.30.30", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39015-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39015-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39015-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 0, "direction": "upstream", "id": "P39015-1.55.55", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39015-1.73.73", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKTDTKKKVNQGWGDDKKEL", "down_seq": "AEKEAQADAAAEIAEDAAEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser118" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DAAAEIAEDAAEAEDAGKPK", "down_seq": "AQLSLQDYLNQQANNQFNKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr146" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P39015-1.150.150", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIAEDAAEAEDAGKPKTAQL", "down_seq": "LQDYLNQQANNQFNKVPEAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser150" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39015-1.146.146", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NQFNKVPEAKKVELDAERIE", "down_seq": "AEKEAYVPATKVKNVKSKQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Thr181" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P39015-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39015-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39015-1.198.198", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PEAKKVELDAERIETAEKEA", "down_seq": "VPATKVKNVKSKQLKTKEYL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr187" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39015-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39015-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39015-1.198.198", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KVELDAERIETAEKEAYVPA", "down_seq": "KVKNVKSKQLKTKEYLEFDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr191" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39015-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39015-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39015-1.198.198", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RIETAEKEAYVPATKVKNVK", "down_seq": "KQLKTKEYLEFDATFVESNT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser198" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39015-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39015-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39015-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39015-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39015-1.218.218", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKSKQLKTKEYLEFDATFVE", "down_seq": "NTRKNFGDRNNNSRNNFNNR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser216" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39015-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39015-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39015-1.229.229", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SKQLKTKEYLEFDATFVESN", "down_seq": "RKNFGDRNNNSRNNFNNRRG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Thr218" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39015-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39015-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39015-1.229.229", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FDATFVESNTRKNFGDRNNN", "down_seq": "RNNFNNRRGGRGARKGNNTA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser229" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39015-1.216.216", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39015-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39015-1.248.248", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSRNNFNNRRGGRGARKGNN", "down_seq": "ANATNSANTVQKNRNIDVSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr248" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39015-1.229.229", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39015-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39015-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39015-1.257.257", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39015-1.267.267", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NFNNRRGGRGARKGNNTANA", "down_seq": "NSANTVQKNRNIDVSNLPSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr252" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39015-1.248.248", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39015-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39015-1.257.257", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39015-1.267.267", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39015-1.271.271", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNRRGGRGARKGNNTANATN", "down_seq": "ANTVQKNRNIDVSNLPSLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser254" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39015-1.248.248", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39015-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39015-1.257.257", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39015-1.267.267", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39015-1.271.271", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RGGRGARKGNNTANATNSAN", "down_seq": "VQKNRNIDVSNLPSLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr257" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39015-1.248.248", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39015-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39015-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39015-1.267.267", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39015-1.271.271", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTANATNSANTVQKNRNIDV", "down_seq": "NLPSLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser267" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39015-1.248.248", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39015-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39015-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39015-1.257.257", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39015-1.271.271", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ATNSANTVQKNRNIDVSNLP", "down_seq": "LA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser271" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39015-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39015-1.254.254", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39015-1.257.257", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39015-1.267.267", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGNDVEDADVVVLPPKEIVK", "down_seq": "NTSSKKADVPPPSADPSKAR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser28" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P39015-1.30.30", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39015-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39015-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39015-1.45.45", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "NPFDLLGNDVEDADVVVLPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NDVEDADVVVLPPKEIVKSN", "down_seq": "SSKKADVPPPSADPSKARKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr30" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39015-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39015-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39015-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39015-1.45.45", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VEDADVVVLPPKEIVKSNTS", "down_seq": "KKADVPPPSADPSKARKNRP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Ser32" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39015-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39015-1.30.30", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39015-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39015-1.45.45", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPKEIVKSNTSSKKADVPPP", "down_seq": "ADPSKARKNRPRPSGNEGAI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Ser41" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39015-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39015-1.30.30", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39015-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39015-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39015-1.55.55", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IVKSNTSSKKADVPPPSADP", "down_seq": "KARKNRPRPSGNEGAIRDKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Ser45" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39015-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39015-1.30.30", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39015-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39015-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39015-1.55.55", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ADVPPPSADPSKARKNRPRP", "down_seq": "GNEGAIRDKTAGRRNNRSKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Ser55" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "downstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39015-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39015-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39015-1.73.73", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.", "journal": "The EMBO journal", "date": "2023", "authors": "Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ] } ], "crossref": [ { "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RPSGNEGAIRDKTAGRRNNR", "down_seq": "KDVTDSATTKKSNTRRATDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "36691768", "url": "https://glygen.org/publication/PubMed/36691768" } ], "site_lbl": "Ser73" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39015-1.41.55", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39015-1.55.55", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39015-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39015-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39015-1.82.82", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAIRDKTAGRRNNRSKDVTD", "down_seq": "ATTKKSNTRRATDRHSRTGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser79" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39015-1.73.73", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39015-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39015-1.82.82", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39015-1.95.95", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IRDKTAGRRNNRSKDVTDSA", "down_seq": "TKKSNTRRATDRHSRTGKTD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Thr81" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39015-1.73.73", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39015-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39015-1.82.82", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39015-1.95.95", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RDKTAGRRNNRSKDVTDSAT", "down_seq": "KKSNTRRATDRHSRTGKTDT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Thr82" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39015-1.73.73", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39015-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39015-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39015-1.95.95", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39015-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "P39015-1", "length": 273, "uniprot_id": "STM1_YEAST", "protein_name": "Suppressor protein STM1", "refseq_ac": "NP_013251", "refseq_name": "Stm1p", "gene_name": "STM1", "gene_names_uniprotkb": "STM1; L9634.1; MPT4; STO1", "gene_names_refseq": "MPT4; STM1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39015", "url": "https://www.uniprot.org/uniprotkb/P39015" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DVTDSATTKKSNTRRATDRH", "down_seq": "RTGKTDTKKKVNQGWGDDKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004140", "url": "https://www.yeastgenome.org/locus/S000004140" }, { "database": "iPTMnet", "id": "P39015", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39015" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser95" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "41", "end_pos": "55" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39015-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39015-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39015-1.82.82", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSNSGVNTSSLIMETPSSSV", "down_seq": "PAASLRNFSNSNNAASKCGV", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr167", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr167" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39016-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39016-1.176.176", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39016-1.178.178", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39016-1.183.183", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39016", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016" }, { "database": "O-GlcNAc Atlas", "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLIMETPSSSVTPAASLRNF", "down_seq": "NSNNAASKCGVDNSSFGLSS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser176", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39016", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39016" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser176" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39016-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39016-1.178.178", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39016-1.183.183", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39016", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016" }, { "database": "O-GlcNAc Atlas", "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IMETPSSSVTPAASLRNFSN", "down_seq": "NNAASKCGVDNSSFGLSSST", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser178", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39016", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39016" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39016-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39016-1.176.176", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39016-1.183.183", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39016", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016" }, { "database": "O-GlcNAc Atlas", "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSSVTPAASLRNFSNSNNAA", "down_seq": "KCGVDNSSFGLSSSTSSSMV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser183", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39016", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39016" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39016-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39016-1.176.176", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39016-1.178.178", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SYNHQPQLSINSVQSLLEPV", "down_seq": "PPPLGQMNNKRNHQKAHSLD", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr47", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr47" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P39016-1.65.65", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.834.834", "start_pos": 834, "end_pos": 834, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39016", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016" }, { "database": "O-GlcNAc Atlas", "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSLSMKSQHIGQGPYNQVNM", "down_seq": "RNASISNMPAMNTARTSDEL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser834", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39016", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39016" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser834" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39016-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39016-1.838.838", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39016", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016" }, { "database": "O-GlcNAc Atlas", "id": "P39016", "url": "https://oglcnac.org/atlas/detail/P39016" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39016", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39016" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAILPLINEFDLEMDGPRRK", "down_seq": "SHDFTVVAPSNSGVNTSSLI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser138" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P39016-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39016-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AILPLINEFDLEMDGPRRKS", "down_seq": "HDFTVVAPSNSGVNTSSLIM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser139" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P39016-1.138.138", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39016-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LINEFDLEMDGPRRKSSHDF", "down_seq": "VVAPSNSGVNTSSLIMETPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr143" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P39016-1.138.138", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39016-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLEMDGPRRKSSHDFTVVAP", "down_seq": "NSGVNTSSLIMETPSSSVTP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ], "site_lbl": "Ser148" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39016-1.138.138", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39016-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39016-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EMDGPRRKSSHDFTVVAPSN", "down_seq": "GVNTSSLIMETPSSSVTPAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ], "site_lbl": "Ser150" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39016-1.138.138", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39016-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39016-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKSSHDFTVVAPSNSGVNTS", "down_seq": "LIMETPSSSVTPAASLRNFS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" } ], "site_lbl": "Ser156" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39016-1.138.138", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39016-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39016-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39016-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39016-1.176.176", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVVAPSNSGVNTSSLIMETP", "down_seq": "SSVTPAASLRNFSNSNNAAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser163" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39016-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39016-1.148.148", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39016-1.150.150", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39016-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39016-1.176.176", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39016-1.178.178", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39016-1.183.183", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVNTSSLIMETPSSSVTPAA", "down_seq": "LRNFSNSNNAASKCGVDNSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser171" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39016-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39016-1.163.163", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39016-1.167.167", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39016-1.176.176", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39016-1.178.178", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39016-1.183.183", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.607.607", "start_pos": 607, "end_pos": 607, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIKLKVKAYAEATGIPFTDI", "down_seq": "PQVTAMSHNNLQTINNENKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser607" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P39016-1.614.614", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.614.614", "start_pos": 614, "end_pos": 614, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AYAEATGIPFTDISPQVTAM", "down_seq": "HNNLQTINNENKNPHNKNSH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser614" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P39016-1.607.607", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVTPPPLGQMNNKRNHQKAH", "down_seq": "LDLSGFNQFISSTQSPLALM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser65" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39016-1.47.47", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.662.662", "start_pos": 662, "end_pos": 662, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HNHAHNNNNNNNQKSHTRHF", "down_seq": "LPANAYHRRSNSSVTNNFSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser662" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P39016-1.672.672", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39016-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39016-1.675.675", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39016-1.677.677", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.672.672", "start_pos": 672, "end_pos": 672, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNQKSHTRHFSLPANAYHRR", "down_seq": "NSSVTNNFSNQYAQDQKIHS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser672" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39016-1.662.662", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39016-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39016-1.675.675", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39016-1.677.677", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39016-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39016-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.674.674", "start_pos": 674, "end_pos": 674, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKSHTRHFSLPANAYHRRSN", "down_seq": "SVTNNFSNQYAQDQKIHSPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser674" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39016-1.662.662", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39016-1.672.672", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39016-1.675.675", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39016-1.677.677", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39016-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39016-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.675.675", "start_pos": 675, "end_pos": 675, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSHTRHFSLPANAYHRRSNS", "down_seq": "VTNNFSNQYAQDQKIHSPQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser675" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39016-1.662.662", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39016-1.672.672", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39016-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39016-1.677.677", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39016-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39016-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.677.677", "start_pos": 677, "end_pos": 677, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HTRHFSLPANAYHRRSNSSV", "down_seq": "NNFSNQYAQDQKIHSPQQIM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr677" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39016-1.662.662", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39016-1.672.672", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39016-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39016-1.675.675", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39016-1.684.684", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39016-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.684.684", "start_pos": 684, "end_pos": 684, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PANAYHRRSNSSVTNNFSNQ", "down_seq": "AQDQKIHSPQQIMNFNQNAY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr684" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39016-1.672.672", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39016-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39016-1.675.675", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39016-1.677.677", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39016-1.692.692", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.692.692", "start_pos": 692, "end_pos": 692, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNSSVTNNFSNQYAQDQKIH", "down_seq": "PQQIMNFNQNAYPSMGAPSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser692" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39016-1.672.672", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39016-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39016-1.675.675", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39016-1.677.677", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39016-1.684.684", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.725.725", "start_pos": 725, "end_pos": 725, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSMGAPSFNSQTNPPLVSHN", "down_seq": "LQNFDNRQFANLMAHPNSAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser725" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P39016-1.743.743", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.743.743", "start_pos": 743, "end_pos": 743, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HNSLQNFDNRQFANLMAHPN", "down_seq": "AAPIHSFSSSNITNVNPNVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser743" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39016-1.725.725", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39016-1.749.749", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39016-1.751.751", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39016-1.752.752", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39016-1.753.753", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39016-1.756.756", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.749.749", "start_pos": 749, "end_pos": 749, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FDNRQFANLMAHPNSAAPIH", "down_seq": "FSSSNITNVNPNVSRGFKQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Ser749" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39016-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39016-1.751.751", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39016-1.752.752", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39016-1.753.753", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39016-1.756.756", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.751.751", "start_pos": 751, "end_pos": 751, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NRQFANLMAHPNSAAPIHSF", "down_seq": "SSNITNVNPNVSRGFKQPGF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser751" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39016-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39016-1.749.749", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39016-1.752.752", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39016-1.753.753", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39016-1.756.756", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.752.752", "start_pos": 752, "end_pos": 752, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQFANLMAHPNSAAPIHSFS", "down_seq": "SNITNVNPNVSRGFKQPGFM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser752" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39016-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39016-1.749.749", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39016-1.751.751", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39016-1.753.753", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39016-1.756.756", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.753.753", "start_pos": 753, "end_pos": 753, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QFANLMAHPNSAAPIHSFSS", "down_seq": "NITNVNPNVSRGFKQPGFMM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Ser753" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39016-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39016-1.749.749", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39016-1.751.751", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39016-1.752.752", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39016-1.756.756", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.756.756", "start_pos": 756, "end_pos": 756, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NLMAHPNSAAPIHSFSSSNI", "down_seq": "NVNPNVSRGFKQPGFMMNET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Thr756" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39016-1.743.743", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39016-1.749.749", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39016-1.751.751", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39016-1.752.752", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39016-1.753.753", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.820.820", "start_pos": 820, "end_pos": 820, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VPRMQYQTEGANWDSSLSMK", "down_seq": "QHIGQGPYNQVNMSRNASIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" } ], "site_lbl": "Ser820" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P39016-1.834.834", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39016-1.838.838", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39016-1.838.838", "start_pos": 838, "end_pos": 838, "uniprot_canonical_ac": "P39016-1", "length": 859, "uniprot_id": "MPT5_YEAST", "protein_name": "Suppressor protein MPT5", "refseq_ac": "NP_011337", "refseq_name": "Mpt5p", "gene_name": "MPT5", "gene_names_uniprotkb": "MPT5; BIC834; HTR1; PUF5", "gene_names_refseq": "HTR1; MPT5; PUF5; UTH4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MKSQHIGQGPYNQVNMSRNA", "down_seq": "ISNMPAMNTARTSDELQFTL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39016", "url": "https://www.uniprot.org/uniprotkb/P39016" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39016", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39016" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003146", "url": "https://www.yeastgenome.org/locus/S000003146" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser838" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "167", "end_pos": "167" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "834", "end_pos": "834" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "614", "end_pos": "614" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "684", "end_pos": "684" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "751", "end_pos": "751" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39016-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39016-1.834.834", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39111-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P39111-1", "length": 118, "uniprot_id": "VATF_YEAST", "protein_name": "V-type proton ATPase subunit F", "refseq_ac": "NP_011534", "refseq_name": "H(+)-transporting V1 sector ATPase subunit F", "gene_name": "VMA7", "gene_names_uniprotkb": "VMA7", "gene_names_refseq": "VMA7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39111", "url": "https://www.uniprot.org/uniprotkb/P39111" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003252", "url": "https://www.yeastgenome.org/locus/S000003252", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AVIADEDTTTGLLLAGIGQI", "down_seq": "PETQEKNFFVYQEGKTTKEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003252", "url": "https://www.yeastgenome.org/locus/S000003252" }, { "database": "iPTMnet", "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr29" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39111-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P39111-1", "length": 118, "uniprot_id": "VATF_YEAST", "protein_name": "V-type proton ATPase subunit F", "refseq_ac": "NP_011534", "refseq_name": "H(+)-transporting V1 sector ATPase subunit F", "gene_name": "VMA7", "gene_names_uniprotkb": "VMA7", "gene_names_refseq": "VMA7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39111", "url": "https://www.uniprot.org/uniprotkb/P39111" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003252", "url": "https://www.yeastgenome.org/locus/S000003252", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DIAILLINQHIAENIRARVD", "down_seq": "FTNAFPAILEIPSKDHPYDP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003252", "url": "https://www.yeastgenome.org/locus/S000003252" }, { "database": "iPTMnet", "id": "P39111", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39111" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser83" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "29", "end_pos": "29" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GTSNILFAKKYGVKPIGTVA", "down_seq": "EWVMGVASISEDYLHANKNA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "His", "comment": "Phosphohistidine; by autocatalysis", "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "site_lbl": "His232" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P39683-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DFLKSFRPPYSDAYVGVRQD", "down_seq": "GDPVEYTKKISHHYHDVLKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser297" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HHYHDVLKLPKFSKIICYSD", "down_seq": "LNVEKAITYSHAAKENGMLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser329" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NGMLATFGIGTNFTNDFRKK", "down_seq": "EPQVKSEPLNIVIKLLEVNG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser365" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P39683-1.371.371", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FGIGTNFTNDFRKKSEPQVK", "down_seq": "EPLNIVIKLLEVNGNHAIKI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser371" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39683-1.365.365", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.418.418", "start_pos": 418, "end_pos": 418, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NMGDPATVKRVKEELGYTER", "down_seq": "WSGDNEAHRWT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser418" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P39683-1.420.420", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDPATVKRVKEELGYTERSW", "down_seq": "GDNEAHRWT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser420" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39683-1.418.418", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSEPVIK", "down_seq": "LLDTDMYKITMHAAVFTNFP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser8" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39683-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "P39683-1", "length": 429, "uniprot_id": "NPT1_YEAST", "protein_name": "Nicotinate phosphoribosyltransferase", "refseq_ac": "NP_014852", "refseq_name": "nicotinate phosphoribosyltransferase", "gene_name": "NPT1", "gene_names_uniprotkb": "NPT1", "gene_names_refseq": "NPT1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39683", "url": "https://www.uniprot.org/uniprotkb/P39683" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EYLKQEIPYLPSAYIKYISS", "down_seq": "NYKLHPEEQISFTSEEIEGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005735", "url": "https://www.yeastgenome.org/locus/S000005735" }, { "database": "iPTMnet", "id": "P39683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39683" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser91" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGEQKSAEGNNIDQSLILKE", "down_seq": "GSTPISISNAPTFNPKYDTS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser177", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser177" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQKSAEGNNIDQSLILKESG", "down_seq": "TPISISNAPTFNPKYDTSNA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser179", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser179" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QKSAEGNNIDQSLILKESGS", "down_seq": "PISISNAPTFNPKYDTSNAS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr180", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr180" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEGNNIDQSLILKESGSTPI", "down_seq": "ISNAPTFNPKYDTSNASMNT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser183", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser183" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNNIDQSLILKESGSTPISI", "down_seq": "NAPTFNPKYDTSNASMNTTL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser185", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser185" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ESGSTPISISNAPTFNPKYD", "down_seq": "SNASMNTTLGSIGSRKYSFN", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr196", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr196" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGSTPISISNAPTFNPKYDT", "down_seq": "NASMNTTLGSIGSRKYSFNY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser197", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser197" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPISISNAPTFNPKYDTSNA", "down_seq": "MNTTLGSIGSRKYSFNYSSL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser200", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser200" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APTFNPKYDTSNASMNTTLG", "down_seq": "IGSRKYSFNYSSLPSPYKTT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser207", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser207" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FNPKYDTSNASMNTTLGSIG", "down_seq": "RKYSFNYSSLPSPYKTTVYR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser210", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LPSPYKTTVYRYSAAKKIPD", "down_seq": "YTANTSAQSIASAKSVRSGV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr240", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPYKTTVYRYSAAKKIPDTY", "down_seq": "ANTSAQSIASAKSVRSGVSK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr242", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Thr242" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTVYRYSAAKKIPDTYTANT", "down_seq": "AQSIASAKSVRSGVSKSAPS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser246", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser246" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.266.266", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YRYSAAKKIPDTYTANTSAQ", "down_seq": "IASAKSVRSGVSKSAPSKKI", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser249", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser249" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.266.266", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAAKKIPDTYTANTSAQSIA", "down_seq": "AKSVRSGVSKSAPSKKISNT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser252", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser252" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.266.266", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.394.394", "start_pos": 394, "end_pos": 394, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNVVVAETSPEKKDGGDKPP", "down_seq": "SAFNFSFNTSRNVEPTENAY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser394", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.400.400", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.404.404", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.395.395", "start_pos": 395, "end_pos": 395, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NVVVAETSPEKKDGGDKPPS", "down_seq": "AFNFSFNTSRNVEPTENAYK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser395", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.394.394", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.400.400", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.404.404", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETSPEKKDGGDKPPSSAFNF", "down_seq": "FNTSRNVEPTENAYKSENAP", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser400", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser400" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.394.394", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.404.404", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.416.416", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EKKDGGDKPPSSAFNFSFNT", "down_seq": "RNVEPTENAYKSENAPSASS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser404", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39705-1.394.394", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.400.400", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.416.416", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.421.421", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSMPGGYFHSEISPDSTVNR", "down_seq": "VVVSAVGEARNDIENKEEEY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser89", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser89" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.109.109", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGYFHSEISPDSTVNRSVVV", "down_seq": "AVGEARNDIENKEEEYDETH", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser93", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39705" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser93" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.112.112", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" }, { "database": "O-GlcNAc Atlas", "id": "P39705", "url": "https://oglcnac.org/atlas/detail/P39705" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39705", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P39705-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.10.10", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.15.15", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SVVVSAVGEARNDIENKEEE", "down_seq": "DETHETNISNAKLANFFSKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr109" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.112.112", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.118.118", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MHRKSLRRA", "down_seq": "ATVPSAPYRKQIISNAHNKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser10" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39705-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.15.15", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VSAVGEARNDIENKEEEYDE", "down_seq": "HETNISNAKLANFFSKKGNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr112" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.118.118", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARNDIENKEEEYDETHETNI", "down_seq": "NAKLANFFSKKGNEPLSEIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser118" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39705-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.112.112", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MHRKSLRRASA", "down_seq": "VPSAPYRKQIISNAHNKPSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr12" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39705-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.10.10", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.15.15", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPLSEIEIEGVMSLLQKSSK", "down_seq": "MITSEGEQKSAEGNNIDQSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser152" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P39705-1.155.155", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SEIEIEGVMSLLQKSSKSMI", "down_seq": "SEGEQKSAEGNNIDQSLILK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr155" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39705-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIEIEGVMSLLQKSSKSMIT", "down_seq": "EGEQKSAEGNNIDQSLILKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser156" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39705-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.155.155", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MHRKSLRRASATVP", "down_seq": "APYRKQIISNAHNKPSLFSK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Ser15" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39705-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.10.10", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.12.12", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VMSLLQKSSKSMITSEGEQK", "down_seq": "AEGNNIDQSLILKESGSTPI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser162" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39705-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.155.155", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSMITSEGEQKSAEGNNIDQ", "down_seq": "LILKESGSTPISISNAPTFN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser171" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39705-1.155.155", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.156.156", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DQSLILKESGSTPISISNAP", "down_seq": "FNPKYDTSNASMNTTLGSIG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr189" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LKESGSTPISISNAPTFNPK", "down_seq": "DTSNASMNTTLGSIGSRKYS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr194" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39705-1.177.177", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.179.179", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.180.180", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SISNAPTFNPKYDTSNASMN", "down_seq": "TLGSIGSRKYSFNYSSLPSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr203" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.183.183", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ISNAPTFNPKYDTSNASMNT", "down_seq": "LGSIGSRKYSFNYSSLPSPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr204" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.185.185", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.189.189", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YDTSNASMNTTLGSIGSRKY", "down_seq": "FNYSSLPSPYKTTVYRYSAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser214" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.196.196", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.197.197", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NASMNTTLGSIGSRKYSFNY", "down_seq": "SLPSPYKTTVYRYSAAKKIP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser218" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASMNTTLGSIGSRKYSFNYS", "down_seq": "LPSPYKTTVYRYSAAKKIPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser219" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.200.200", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTTLGSIGSRKYSFNYSSLP", "down_seq": "PYKTTVYRYSAAKKIPDTYT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser222" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser222" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser222" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.203.203", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TLGSIGSRKYSFNYSSLPSP", "down_seq": "KTTVYRYSAAKKIPDTYTAN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" } ], "site_lbl": "Tyr224" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.207.207", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.210.210", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KYSFNYSSLPSPYKTTVYRY", "down_seq": "AAKKIPDTYTANTSAQSIAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" } ], "site_lbl": "Ser232" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.219.219", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.224.224", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KTTVYRYSAAKKIPDTYTAN", "down_seq": "SAQSIASAKSVRSGVSKSAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr245" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39705-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAQSIASAKSVRSGVSKSAP", "down_seq": "KKISNTAAALVSLLDENDSK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser266" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.246.246", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.249.249", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.252.252", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.285.285", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.285.285", "start_pos": 285, "end_pos": 285, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSKKISNTAAALVSLLDEND", "down_seq": "KKNNAASELANPYSSYVSQI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser285" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.266.266", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.301.301", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DENDSKKNNAASELANPYSS", "down_seq": "VSQIRKHKRVSPNAAPRQEI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ], "site_lbl": "Tyr301" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39705-1.285.285", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.312.312", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SELANPYSSYVSQIRKHKRV", "down_seq": "PNAAPRQEISEEETTVKPLF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser312" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39705-1.301.301", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.349.349", "start_pos": 349, "end_pos": 349, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KPLFQNVPEQGEEPMKQLNA", "down_seq": "KISPSAPSKDSFTKYKPARS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr349" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P39705-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.352.352", "start_pos": 352, "end_pos": 352, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FQNVPEQGEEPMKQLNATKI", "down_seq": "PSAPSKDSFTKYKPARSSSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser352" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39705-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQGEEPMKQLNATKISPSAP", "down_seq": "KDSFTKYKPARSSSLRSNVV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser357" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39705-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEPMKQLNATKISPSAPSKD", "down_seq": "FTKYKPARSSSLRSNVVVAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser360" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39705-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.362.362", "start_pos": 362, "end_pos": 362, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PMKQLNATKISPSAPSKDSF", "down_seq": "KYKPARSSSLRSNVVVAETS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr362" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39705-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.369.369", "start_pos": 369, "end_pos": 369, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKISPSAPSKDSFTKYKPAR", "down_seq": "SSLRSNVVVAETSPEKKDGG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" } ], "site_lbl": "Ser369" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.349.349", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39705-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ISPSAPSKDSFTKYKPARSS", "down_seq": "LRSNVVVAETSPEKKDGGDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser371" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.374.374", "start_pos": 374, "end_pos": 374, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAPSKDSFTKYKPARSSSLR", "down_seq": "NVVVAETSPEKKDGGDKPPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser374" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39705-1.357.357", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.394.394", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FTKYKPARSSSLRSNVVVAE", "down_seq": "SPEKKDGGDKPPSSAFNFSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr381" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.382.382", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.394.394", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.400.400", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.382.382", "start_pos": 382, "end_pos": 382, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Mol. Cell. Proteomics", "date": "2005", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKYKPARSSSLRSNVVVAET", "down_seq": "PEKKDGGDKPPSSAFNFSFN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser382" }, { "kinase_uniprot_canonical_ac": "P22216-1", "kinase_gene_name": "RAD53", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser382" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser382" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.362.362", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.369.369", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.371.371", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.374.374", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.381.381", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.394.394", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.395.395", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.400.400", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.416.416", "start_pos": 416, "end_pos": 416, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AFNFSFNTSRNVEPTENAYK", "down_seq": "ENAPSASSKEFNFTNLQAKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser416" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39705-1.400.400", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.404.404", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.421.421", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FNTSRNVEPTENAYKSENAP", "down_seq": "ASSKEFNFTNLQAKPLVGKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser421" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39705-1.404.404", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.416.416", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.450.450", "start_pos": 450, "end_pos": 450, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNLQAKPLVGKPKTELTKGD", "down_seq": "TPVQPDLSVTPQKSSSKGFV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser450" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P39705-1.451.451", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.451.451", "start_pos": 451, "end_pos": 451, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NLQAKPLVGKPKTELTKGDS", "down_seq": "PVQPDLSVTPQKSSSKGFVF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr451" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P39705-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VGKPKTELTKGDSTPVQPDL", "down_seq": "VTPQKSSSKGFVFNSVQKKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser458" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39705-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.451.451", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.478.478", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KPKTELTKGDSTPVQPDLSV", "down_seq": "PQKSSSKGFVFNSVQKKSRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr460" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39705-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.451.451", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39705-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39705-1.480.480", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKGDSTPVQPDLSVTPQKSS", "down_seq": "KGFVFNSVQKKSRSNLSQEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser466" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39705-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39705-1.451.451", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.480.480", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39705-1.483.483", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.473.473", "start_pos": 473, "end_pos": 473, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQPDLSVTPQKSSSKGFVFN", "down_seq": "VQKKSRSNLSQENDNEGKHI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser473" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39705-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.480.480", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.483.483", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.478.478", "start_pos": 478, "end_pos": 478, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVTPQKSSSKGFVFNSVQKK", "down_seq": "RSNLSQENDNEGKHISASID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser478" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39705-1.480.480", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.483.483", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.480.480", "start_pos": 480, "end_pos": 480, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "A proteome-wide analysis of kinase-substrate network in the DNA damage response.", "journal": "The Journal of biological chemistry", "date": "2010-04-23", "authors": "Chen Sheng-hong, Albuquerque Claudio P, Liang Jason, Suhandynata Raymond T, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPQKSSSKGFVFNSVQKKSR", "down_seq": "NLSQENDNEGKHISASIDND", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser480" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39705-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39705-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.483.483", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.483.483", "start_pos": 483, "end_pos": 483, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "A proteome-wide analysis of kinase-substrate network in the DNA damage response.", "journal": "The Journal of biological chemistry", "date": "2010-04-23", "authors": "Chen Sheng-hong, Albuquerque Claudio P, Liang Jason, Suhandynata Raymond T, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSSSKGFVFNSVQKKSRSNL", "down_seq": "QENDNEGKHISASIDNDFSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser483" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39705-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.480.480", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPSLFSKIKTFFTQKDSARV", "down_seq": "PRNNVANKQPRNESFNRRIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser49" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P39705-1.63.63", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MHRK", "down_seq": "LRRASATVPSAPYRKQIISN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser5" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P39705-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.10.10", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.15.15", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDSARVSPRNNVANKQPRNE", "down_seq": "FNRRISSMPGGYFHSEISPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser63" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39705-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PRNNVANKQPRNESFNRRIS", "down_seq": "MPGGYFHSEISPDSTVNRSV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser70" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P39705-1.63.63", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ANKQPRNESFNRRISSMPGG", "down_seq": "FHSEISPDSTVNRSVVVSAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr75" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39705-1.63.63", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QPRNESFNRRISSMPGGYFH", "down_seq": "EISPDSTVNRSVVVSAVGEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser78" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39705-1.63.63", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NESFNRRISSMPGGYFHSEI", "down_seq": "PDSTVNRSVVVSAVGEARND", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser81" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39705-1.63.63", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FNRRISSMPGGYFHSEISPD", "down_seq": "TVNRSVVVSAVGEARNDIEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser84" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39705-1.85.85", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39705-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P39705-1", "length": 539, "uniprot_id": "NUP60_YEAST", "protein_name": "Nucleoporin NUP60", "refseq_ac": "NP_009401", "refseq_name": "FG-nucleoporin NUP60", "gene_name": "NUP60", "gene_names_uniprotkb": "NUP60; FUN17", "gene_names_refseq": "NUP60", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39705", "url": "https://www.uniprot.org/uniprotkb/P39705" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NRRISSMPGGYFHSEISPDS", "down_seq": "VNRSVVVSAVGEARNDIENK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000063", "url": "https://www.yeastgenome.org/locus/S000000063" }, { "database": "iPTMnet", "id": "P39705", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39705" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr85" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39705-1.70.70", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39705-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39705-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39705-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39705-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39705-1.89.89", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39705-1.93.93", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39718-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "P39718-1", "length": 180, "uniprot_id": "PEX22_YEAST", "protein_name": "Ubiquitin-conjugating enzyme E2 enzyme activator PEX22", "refseq_ac": "NP_009346", "refseq_name": "ubiquitin-protein transferase activating protein PEX22", "gene_name": "PEX22", "gene_names_uniprotkb": "PEX22", "gene_names_refseq": "PEX22; YAF5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39718", "url": "https://www.uniprot.org/uniprotkb/P39718" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Insights into ubiquitin-conjugating enzyme/ co-activator interactions from the structure of the Pex4p:Pex22p complex.", "journal": "The EMBO journal", "date": "2012-01-18", "authors": "Williams Chris, van den Berg Marlene, Panjikar Santosh, Stanley Will A, Distel Ben, Wilmanns Matthias", "evidence": [ { "database": "UniProtKB", "id": "P39718", "url": "https://www.uniprot.org/uniprotkb/P39718" } ], "reference": [ { "type": "PubMed", "id": "22085930", "url": "https://glygen.org/publication/PubMed/22085930" } ] } ], "crossref": [ { "id": "P39718", "url": "https://www.uniprot.org/uniprotkb/P39718", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22085930", "url": "https://glygen.org/publication/PubMed/22085930", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HKIIYCDSMDGLWSCVRRLG", "down_seq": "FQCILNSRDFTSSGGSDAAV", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Decreases binding to PEX4.", "evidence": [ { "database": "UniProtKB", "id": "P39718", "url": "https://www.uniprot.org/uniprotkb/P39718" }, { "database": "PubMed", "id": "22085930", "url": "https://glygen.org/publication/PubMed/22085930" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "133", "end_pos": "133" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.468.468", "start_pos": 468, "end_pos": 468, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKKKPSITKLPASSSPSPSP", "down_seq": "SSASPSRQASLESIRTRARA", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr468", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr468" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RDKALYLEVKNAKSKLKKKP", "down_seq": "ITKLPASSSPSPSPTSSASP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser453" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVKNAKSKLKKKPSITKLPA", "down_seq": "SSPSPSPTSSASPSRQASLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser460" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.461.461", "start_pos": 461, "end_pos": 461, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKNAKSKLKKKPSITKLPAS", "down_seq": "SPSPSPTSSASPSRQASLES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser461" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KNAKSKLKKKPSITKLPASS", "down_seq": "PSPSPTSSASPSRQASLESI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser462" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKSKLKKKPSITKLPASSSP", "down_seq": "PSPTSSASPSRQASLESIRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser464" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKLKKKPSITKLPASSSPSP", "down_seq": "PTSSASPSRQASLESIRTRA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser466" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.469.469", "start_pos": 469, "end_pos": 469, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKKPSITKLPASSSPSPSPT", "down_seq": "SASPSRQASLESIRTRARAH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser469" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.470.470", "start_pos": 470, "end_pos": 470, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKPSITKLPASSSPSPSPTS", "down_seq": "ASPSRQASLESIRTRARAHL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser470" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.472.472", "start_pos": 472, "end_pos": 472, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSITKLPASSSPSPSPTSSA", "down_seq": "PSRQASLESIRTRARAHLAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser472" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39732-1.453.453", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ITKLPASSSPSPSPTSSASP", "down_seq": "RQASLESIRTRARAHLASNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser474" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.478.478", "start_pos": 478, "end_pos": 478, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PASSSPSPSPTSSASPSRQA", "down_seq": "LESIRTRARAHLASNSSRSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser478" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39732-1.460.460", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.481.481", "start_pos": 481, "end_pos": 481, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSPSPSPTSSASPSRQASLE", "down_seq": "IRTRARAHLASNSSRSPSVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser481" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39732-1.461.461", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P39732-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39732-1.464.464", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39732-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39732-1.468.468", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39732-1.469.469", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39732-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39732-1.499.499", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.492.492", "start_pos": 492, "end_pos": 492, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPSRQASLESIRTRARAHLA", "down_seq": "NSSRSPSVSPVRTTFNNKNA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser492" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39732-1.472.472", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.499.499", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRQASLESIRTRARAHLASN", "down_seq": "SRSPSVSPVRTTFNNKNAET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser494" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39732-1.474.474", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.499.499", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.495.495", "start_pos": 495, "end_pos": 495, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQASLESIRTRARAHLASNS", "down_seq": "RSPSVSPVRTTFNNKNAETK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser495" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.499.499", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASLESIRTRARAHLASNSSR", "down_seq": "PSVSPVRTTFNNKNAETKKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser497" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39732-1.478.478", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.499.499", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.499.499", "start_pos": 499, "end_pos": 499, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LESIRTRARAHLASNSSRSP", "down_seq": "VSPVRTTFNNKNAETKKSVV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser499" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.501.501", "start_pos": 501, "end_pos": 501, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SIRTRARAHLASNSSRSPSV", "down_seq": "PVRTTFNNKNAETKKSVVSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser501" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39732-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39732-1.492.492", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39732-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.499.499", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39732-1.520.520", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.520.520", "start_pos": 520, "end_pos": 520, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSPVRTTFNNKNAETKKSVV", "down_seq": "PEKRKLINGRRPRSSSLQSY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser520" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39732-1.501.501", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39732-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39732-1.535.535", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39732-1.536.536", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39732-1.539.539", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.534.534", "start_pos": 534, "end_pos": 534, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKKSVVSPEKRKLINGRRPR", "down_seq": "SSLQSYTNKQQTSYLNSTRH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Ser534" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39732-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.535.535", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.536.536", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.539.539", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKSVVSPEKRKLINGRRPRS", "down_seq": "SLQSYTNKQQTSYLNSTRHP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser535" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39732-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.536.536", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.539.539", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSVVSPEKRKLINGRRPRSS", "down_seq": "LQSYTNKQQTSYLNSTRHPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser536" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39732-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.535.535", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.539.539", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.539.539", "start_pos": 539, "end_pos": 539, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSPEKRKLINGRRPRSSSLQ", "down_seq": "YTNKQQTSYLNSTRHPSIAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser539" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39732-1.520.520", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.535.535", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.536.536", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.568.568", "start_pos": 568, "end_pos": 568, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YLNSTRHPSIAPPSKLNNQR", "down_seq": "NSLQSSTMTLNQKIVQDTVR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ], "site_lbl": "Ser568" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P39732-1.570.570", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.574.574", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.570.570", "start_pos": 570, "end_pos": 570, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSTRHPSIAPPSKLNNQRSN", "down_seq": "LQSSTMTLNQKIVQDTVRHL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser570" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39732-1.568.568", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.574.574", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.574.574", "start_pos": 574, "end_pos": 574, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HPSIAPPSKLNNQRSNSLQS", "down_seq": "TMTLNQKIVQDTVRHLMNKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser574" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39732-1.568.568", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.570.570", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.594.594", "start_pos": 594, "end_pos": 594, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STMTLNQKIVQDTVRHLMNK", "down_seq": "ASTPNPSASSSLAPSPKVSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser594" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39732-1.574.574", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39732-1.603.603", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39732-1.604.604", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39732-1.605.605", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39732-1.609.609", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.597.597", "start_pos": 597, "end_pos": 597, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TLNQKIVQDTVRHLMNKSAS", "down_seq": "PNPSASSSLAPSPKVSSINN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr597" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.603.603", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39732-1.604.604", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.605.605", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39732-1.609.609", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.601.601", "start_pos": 601, "end_pos": 601, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIVQDTVRHLMNKSASTPNP", "down_seq": "ASSSLAPSPKVSSINNTSSG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser601" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.603.603", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.604.604", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.605.605", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39732-1.609.609", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.603.603", "start_pos": 603, "end_pos": 603, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQDTVRHLMNKSASTPNPSA", "down_seq": "SSLAPSPKVSSINNTSSGKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser603" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.604.604", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39732-1.605.605", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39732-1.609.609", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.604.604", "start_pos": 604, "end_pos": 604, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDTVRHLMNKSASTPNPSAS", "down_seq": "SLAPSPKVSSINNTSSGKSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser604" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39732-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.603.603", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39732-1.605.605", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39732-1.609.609", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.605.605", "start_pos": 605, "end_pos": 605, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DTVRHLMNKSASTPNPSASS", "down_seq": "LAPSPKVSSINNTSSGKSSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser605" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39732-1.603.603", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39732-1.604.604", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.609.609", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.609.609", "start_pos": 609, "end_pos": 609, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLMNKSASTPNPSASSSLAP", "down_seq": "PKVSSINNTSSGKSSSTLIA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser609" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39732-1.594.594", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39732-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39732-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39732-1.603.603", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39732-1.604.604", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39732-1.605.605", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.648.648", "start_pos": 648, "end_pos": 648, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IANSSDTLAIETLTLDPESN", "down_seq": "SELSIKRVRFAGVPPMTEAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser648" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P39732-1.649.649", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39732-1.652.652", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.649.649", "start_pos": 649, "end_pos": 649, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ANSSDTLAIETLTLDPESNS", "down_seq": "ELSIKRVRFAGVPPMTEAEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser649" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P39732-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39732-1.652.652", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39732-1.652.652", "start_pos": 652, "end_pos": 652, "uniprot_canonical_ac": "P39732-1", "length": 760, "uniprot_id": "GIP4_YEAST", "protein_name": "GLC7-interacting protein 4", "refseq_ac": "NP_009371", "refseq_name": "protein phosphatase regulator GIP4", "gene_name": "GIP4", "gene_names_uniprotkb": "GIP4; FUN21", "gene_names_refseq": "FUN21; GIP4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39732", "url": "https://www.uniprot.org/uniprotkb/P39732" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SDTLAIETLTLDPESNSSEL", "down_seq": "IKRVRFAGVPPMTEAENPKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000029", "url": "https://www.yeastgenome.org/locus/S000000029" }, { "database": "iPTMnet", "id": "P39732", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39732" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser652" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "468", "end_pos": "468" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "453", "end_pos": "453" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "478", "end_pos": "478" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "605", "end_pos": "605" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "652", "end_pos": "652" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39732-1.648.648", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39732-1.649.649", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39904-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P39904-1", "length": 641, "uniprot_id": "VPS52_YEAST", "protein_name": "Vacuolar protein sorting-associated protein 52", "refseq_ac": "NP_010772", "refseq_name": "Vps52p", "gene_name": "VPS52", "gene_names_uniprotkb": "VPS52; D8035.27; SAC2", "gene_names_refseq": "SAC2; VPS52", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904" }, { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002892", "url": "https://www.yeastgenome.org/locus/S000002892", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DPFENYLKDCKFKAPSNKDQ", "down_seq": "PFAKLKSLQETHSNNEAAIN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002892", "url": "https://www.yeastgenome.org/locus/S000002892" }, { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser51" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39904-1.602.602", "start_pos": 602, "end_pos": 602, "uniprot_canonical_ac": "P39904-1", "length": 641, "uniprot_id": "VPS52_YEAST", "protein_name": "Vacuolar protein sorting-associated protein 52", "refseq_ac": "NP_010772", "refseq_name": "Vps52p", "gene_name": "VPS52", "gene_names_uniprotkb": "VPS52; D8035.27; SAC2", "gene_names_refseq": "SAC2; VPS52", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904" }, { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000002892", "url": "https://www.yeastgenome.org/locus/S000002892", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQLHLHLNINDSDAQNYNFD", "down_seq": "AENVGTKVANDDDNDSSVPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" }, { "database": "SGD", "id": "S000002892", "url": "https://www.yeastgenome.org/locus/S000002892" } ], "site_lbl": "Ser602" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39904-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "P39904-1", "length": 641, "uniprot_id": "VPS52_YEAST", "protein_name": "Vacuolar protein sorting-associated protein 52", "refseq_ac": "NP_010772", "refseq_name": "Vps52p", "gene_name": "VPS52", "gene_names_uniprotkb": "VPS52; D8035.27; SAC2", "gene_names_refseq": "SAC2; VPS52", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39904", "url": "https://www.uniprot.org/uniprotkb/P39904" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002892", "url": "https://www.yeastgenome.org/locus/S000002892", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MDVLKEVL", "down_seq": "LDQDKFDQLKETSRDKTNET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002892", "url": "https://www.yeastgenome.org/locus/S000002892" }, { "database": "iPTMnet", "id": "P39904", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39904" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser9" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "EGTMESMEQQLFSIESANLN", "down_seq": "ETMRAMQEGAKAMKTIHSGL", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "E", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GTMESMEQQLFSIESANLNL", "down_seq": "TMRAMQEGAKAMKTIHSGLD", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Leads to severe sorting defects; when associated with K-95 and K-109.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TMESMEQQLFSIESANLNLE", "down_seq": "MRAMQEGAKAMKTIHSGLDI", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "E", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "MESMEQQLFSIESANLNLET", "down_seq": "RAMQEGAKAMKTIHSGLDID", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "E", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "MEQQLFSIESANLNLETMRA", "down_seq": "QEGAKAMKTIHSGLDIDKVD", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "E", "comment": "Leads to severe sorting defects. Impairs the formation of protofilaments; when associated with E-52.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QQLFSIESANLNLETMRAMQ", "down_seq": "GAKAMKTIHSGLDIDKVDET", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Leads to severe sorting defects; when associated with K-95 and K-102.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "IESANLNLETMRAMQEGAKA", "down_seq": "KTIHSGLDIDKVDETMDEIR", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "E", "comment": "Leads to severe sorting defects. Impairs the formation of protofilaments; when associated with E-52.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "ANLNLETMRAMQEGAKAMKT", "down_seq": "HSGLDIDKVDETMDEIREQV", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "E", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LETMRAMQEGAKAMKTIHSG", "down_seq": "DIDKVDETMDEIREQVELGD", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LFGWTSSNAKNKESPTKAIV", "down_seq": "LREHINLLSKKQSHLRTQIT", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "E", "comment": "Leads to severe sorting defects; when associated with E-29 and E-36.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39929-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39929-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.29.29", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.36.36", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.45.45", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "TSSNAKNKESPTKAIVRLRE", "down_seq": "INLLSKKQSHLRTQITNQEN", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "E", "comment": "Leads to severe sorting defects; when associated with E-25 and E-36.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39929-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.36.36", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.45.45", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Essential N-terminal insertion motif anchors the ESCRT-III filament during MVB vesicle formation.", "journal": "Developmental cell", "date": "2013-10-28", "authors": "Buchkovich Nicholas J, Henne William Mike, Tang Shaogeng, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "M", "down_seq": "SSLFGWTSSNAKNKESPTKA", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "E", "comment": "Impairs binding to membrane.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P39929-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39929-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.18.18", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KESPTKAIVRLREHINLLSK", "down_seq": "QSHLRTQITNQENEARIFLT", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "E", "comment": "Leads to severe sorting defects; when associated with E-25 and E-29.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39929-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39929-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.29.29", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.52.52", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLSKKQSHLRTQITNQENEA", "down_seq": "IFLTKGNKVMAKNALKKKKT", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "E", "comment": "Impairs the formation of protofilaments; when associated with K-90. Also impairs the formation of protofilaments; when associated with E-94. Also impairs the formation of protofilaments; when associated with E-107. Also impairs the formation of protofilaments; when associated with E-114.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39929-1.36.36", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.72.72", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Essential N-terminal insertion motif anchors the ESCRT-III filament during MVB vesicle formation.", "journal": "Developmental cell", "date": "2013-10-28", "authors": "Buchkovich Nicholas J, Henne William Mike, Tang Shaogeng, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MWSSL", "down_seq": "GWTSSNAKNKESPTKAIVRL", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "E", "comment": "Impairs binding to membrane.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P39929-1.2.2", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.25.25", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AKNALKKKKTIEQLLSKVEG", "down_seq": "MESMEQQLFSIESANLNLET", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "E", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39929-1.72.72", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "LKKKKTIEQLLSKVEGTMES", "down_seq": "EQQLFSIESANLNLETMRAM", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "E", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39929-1.72.72", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Essential N-terminal insertion motif anchors the ESCRT-III filament during MVB vesicle formation.", "journal": "Developmental cell", "date": "2013-10-28", "authors": "Buchkovich Nicholas J, Henne William Mike, Tang Shaogeng, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "MWSSLFG", "down_seq": "TSSNAKNKESPTKAIVRLRE", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "E", "comment": "Impairs binding to membrane.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "24139821", "url": "https://glygen.org/publication/PubMed/24139821" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39929-1.2.2", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.25.25", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "KKTIEQLLSKVEGTMESMEQ", "down_seq": "LFSIESANLNLETMRAMQEG", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "K", "comment": "Leads to severe sorting defects. Impairs the formation of protofilaments; when associated with E-52.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39929-1.72.72", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EQLLSKVEGTMESMEQQLFS", "down_seq": "ESANLNLETMRAMQEGAKAM", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "E", "comment": "Leads to severe sorting defects. Impairs the formation of protofilaments; when associated with E-52.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QLLSKVEGTMESMEQQLFSI", "down_seq": "SANLNLETMRAMQEGAKAMK", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Leads to severe sorting defects; when associated with K-102 and K-109.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LSKVEGTMESMEQQLFSIES", "down_seq": "NLNLETMRAMQEGAKAMKTI", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "K", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments.", "journal": "eLife", "date": "2015-12-15", "authors": "Tang Shaogeng, Henne W Mike, Borbat Peter P, Buchkovich Nicholas J, Freed Jack H, Mao Yuxin, Fromme J Christopher, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "reference": [ { "type": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KVEGTMESMEQQLFSIESAN", "down_seq": "NLETMRAMQEGAKAMKTIHS", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "K", "comment": "Leads to severe sorting defects.", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "26670543", "url": "https://glygen.org/publication/PubMed/26670543" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.94.94", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.95.95", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SANLNLETMRAMQEGAKAMK", "down_seq": "IHSGLDIDKVDETMDEIREQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr116" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39929-1.97.97", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LNLETMRAMQEGAKAMKTIH", "down_seq": "GLDIDKVDETMDEIREQVEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser119" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.99.99", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39929-1.101.101", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39929-1.102.102", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39929-1.103.103", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.104.104", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.107.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EGAKAMKTIHSGLDIDKVDE", "down_seq": "MDEIREQVELGDEISDAISR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr129" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39929-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39929-1.116.116", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.117.117", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.119.119", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39929-1.121.121", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.144.144", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39929-1.148.148", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DKVDETMDEIREQVELGDEI", "down_seq": "DAISRPLITGANEVDEDELD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser144" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39929-1.148.148", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETMDEIREQVELGDEISDAI", "down_seq": "RPLITGANEVDEDELDEELD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser148" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39929-1.129.129", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39929-1.144.144", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MWSSLFGWTSSNAKNKE", "down_seq": "PTKAIVRLREHINLLSKKQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser18" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39929-1.2.2", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39929-1.8.8", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.29.29", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39929-1.36.36", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ENANQETSKIVNNNVNAAPI", "down_seq": "ENKVSLPSVPSNKIKQSENS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser193" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P39929-1.201.201", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39929-1.210.210", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39929-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIVNNNVNAAPISENKVSLP", "down_seq": "VPSNKIKQSENSVKDGEEEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser201" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39929-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.210.210", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39929-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNNVNAAPISENKVSLPSVP", "down_seq": "NKIKQSENSVKDGEEEEDEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser204" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39929-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.201.201", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39929-1.210.210", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39929-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APISENKVSLPSVPSNKIKQ", "down_seq": "ENSVKDGEEEEDEEDEDEKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser210" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39929-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.201.201", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39929-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39929-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SENKVSLPSVPSNKIKQSEN", "down_seq": "VKDGEEEEDEEDEDEKALRE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser213" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39929-1.201.201", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.204.204", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39929-1.210.210", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RLREHINLLSKKQSHLRTQI", "down_seq": "NQENEARIFLTKGNKVMAKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr45" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39929-1.29.29", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39929-1.36.36", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39929-1.52.52", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39929-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "P39929-1", "length": 240, "uniprot_id": "SNF7_YEAST", "protein_name": "Vacuolar-sorting protein SNF7", "refseq_ac": "NP_013125", "refseq_name": "ESCRT-III subunit protein SNF7", "gene_name": "SNF7", "gene_names_uniprotkb": "SNF7; DID1; VPS32", "gene_names_refseq": "DID1; RNS4; SNF7; VPL5; VPS32", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RIFLTKGNKVMAKNALKKKK", "down_seq": "IEQLLSKVEGTMESMEQQLF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P39929", "url": "https://www.uniprot.org/uniprotkb/P39929" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P39929", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39929" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000004015", "url": "https://www.yeastgenome.org/locus/S000004015" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr72" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "72", "end_pos": "72" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39929-1.52.52", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39929-1.83.83", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39929-1.87.87", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39929-1.90.90", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "REEPAPRNDMPSSKTYTNHS", "down_seq": "SFTRSTEPPPVFQMVPGRMM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser131" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P39955-1.132.132", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39955-1.134.134", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEPAPRNDMPSSKTYTNHSS", "down_seq": "FTRSTEPPPVFQMVPGRMMK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser132" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P39955-1.131.131", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39955-1.134.134", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PAPRNDMPSSKTYTNHSSSF", "down_seq": "RSTEPPPVFQMVPGRMMKTL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr134" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39955-1.131.131", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39955-1.132.132", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PGRMMKTLRNRNACGYKTAY", "down_seq": "NPSLSSYGNSTSIKRGEDAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser167" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEDDHDVGILKGHNVFDEEE", "down_seq": "DGFEFDVSDYYDNFSEVDVE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser261" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAPALPSLPPPPLLNVDRAS", "down_seq": "TGALKPHSLETSTTMDSSKI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser355" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P39955-1.363.363", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.363.363", "start_pos": 363, "end_pos": 363, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPPPLLNVDRASSTGALKPH", "down_seq": "LETSTTMDSSKIRNPQISKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser363" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39955-1.355.355", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages.", "journal": "Cell communication and signaling : CCS", "date": "2019-06-17", "authors": "Janschitz Marion, Romanov Natalie, Varnavides Gina, Hollenstein David Maria, G\u00e9recov\u00e1 Gabriela, Ammerer Gustav, Hartl Markus, Reiter Wolfgang", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "31208443", "url": "https://glygen.org/publication/PubMed/31208443" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31208443", "url": "https://glygen.org/publication/PubMed/31208443", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NPQISKLMKNNHVPYLKGTK", "down_seq": "TPTLITKSTPTFITRSKSNT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "31208443", "url": "https://glygen.org/publication/PubMed/31208443" } ], "site_lbl": "Ser397" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P39955-1.415.415", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.415.415", "start_pos": 415, "end_pos": 415, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKSTPTLITKSTPTFITRSK", "down_seq": "NTKPIIKSNASSPTSSLTVP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser415" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39955-1.397.397", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39955-1.423.423", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39955-1.426.426", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39955-1.427.427", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKSTPTFITRSKSNTKPIIK", "down_seq": "NASSPTSSLTVPNSVIQKPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser423" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39955-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39955-1.426.426", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39955-1.427.427", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.426.426", "start_pos": 426, "end_pos": 426, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Novel interconnections of HOG signaling revealed by combined use of two proteomic software packages.", "journal": "Cell communication and signaling : CCS", "date": "2019-06-17", "authors": "Janschitz Marion, Romanov Natalie, Varnavides Gina, Hollenstein David Maria, G\u00e9recov\u00e1 Gabriela, Ammerer Gustav, Hartl Markus, Reiter Wolfgang", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "31208443", "url": "https://glygen.org/publication/PubMed/31208443" } ] } ], "crossref": [ { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31208443", "url": "https://glygen.org/publication/PubMed/31208443", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPTFITRSKSNTKPIIKSNA", "down_seq": "SPTSSLTVPNSVIQKPKTAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "31208443", "url": "https://glygen.org/publication/PubMed/31208443" } ], "site_lbl": "Ser426" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39955-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39955-1.423.423", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39955-1.427.427", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.427.427", "start_pos": 427, "end_pos": 427, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PTFITRSKSNTKPIIKSNAS", "down_seq": "PTSSLTVPNSVIQKPKTAAM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser427" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39955-1.415.415", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39955-1.423.423", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39955-1.426.426", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKPKTAAMAAKRVLNSKKVA", "down_seq": "NPALNTTKKSHPILKSKTAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser460" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NQTTSMSKTNRKIPAQKKIG", "down_seq": "PKIEDVGTEDATEHATSLNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser536" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P39955-1.552.552", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39955-1.553.553", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.552.552", "start_pos": 552, "end_pos": 552, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KKIGSPKIEDVGTEDATEHA", "down_seq": "SLNEQREEPEIDKKVLREIL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr552" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39955-1.536.536", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39955-1.553.553", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39955-1.553.553", "start_pos": 553, "end_pos": 553, "uniprot_canonical_ac": "P39955-1", "length": 897, "uniprot_id": "SAPR1_YEAST", "protein_name": "Microtubule severing ATPase SAP1", "refseq_ac": "NP_010966", "refseq_name": "putative AAA family ATPase SAP1", "gene_name": "SAP1", "gene_names_uniprotkb": "SAP1", "gene_names_refseq": "SAP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39955", "url": "https://www.uniprot.org/uniprotkb/P39955" }, { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIGSPKIEDVGTEDATEHAT", "down_seq": "LNEQREEPEIDKKVLREILE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39955", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39955" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000849", "url": "https://www.yeastgenome.org/locus/S000000849" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser553" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "553", "end_pos": "553" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39955-1.536.536", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39955-1.552.552", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QLMPPANVDQRASYRGHVRK", "down_seq": "SQSLEDLPSQQNFIPTPRNT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr372", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr372" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P39969-1.373.373", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.375.375", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.381.381", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.388.388", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMPPANVDQRASYRGHVRKT", "down_seq": "QSLEDLPSQQNFIPTPRNTR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser373", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser373" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P39969-1.372.372", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.375.375", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.381.381", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.388.388", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPANVDQRASYRGHVRKTSQ", "down_seq": "LEDLPSQQNFIPTPRNTRNS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser375", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser375" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39969-1.372.372", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.373.373", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.381.381", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.388.388", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRASYRGHVRKTSQSLEDLP", "down_seq": "QQNFIPTPRNTRNSSASKHR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser381", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" } ], "site_lbl": "Ser381" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39969-1.372.372", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.373.373", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.375.375", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.388.388", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.488.488", "start_pos": 488, "end_pos": 488, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPAQLYSWQSPTLSFSGPKR", "down_seq": "SYIDQYSSSDSNFNSRSALP", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr488", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr488" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAQLYSWQSPTLSFSGPKRT", "down_seq": "YIDQYSSSDSNFNSRSALPK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser489", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser489" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.495.495", "start_pos": 495, "end_pos": 495, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WQSPTLSFSGPKRTSYIDQY", "down_seq": "SSDSNFNSRSALPKNNQGGG", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser495", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSPTLSFSGPKRTSYIDQYS", "down_seq": "SDSNFNSRSALPKNNQGGGK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser496", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPTLSFSGPKRTSYIDQYSS", "down_seq": "DSNFNSRSALPKNNQGGGKA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser497", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser497" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.499.499", "start_pos": 499, "end_pos": 499, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLSFSGPKRTSYIDQYSSSD", "down_seq": "NFNSRSALPKNNQGGGKALS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser499", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.519.519", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.503.503", "start_pos": 503, "end_pos": 503, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGPKRTSYIDQYSSSDSNFN", "down_seq": "RSALPKNNQGGGKALSPIPS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser503", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser503" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.523.523", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.665.665", "start_pos": 665, "end_pos": 665, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKSSFMLSPFRQQFTDNAAR", "down_seq": "SSPEENPITSMPSEKNSSPI", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser665", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser665" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.675.675", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.678.678", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.683.683", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.666.666", "start_pos": 666, "end_pos": 666, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSSFMLSPFRQQFTDNAARS", "down_seq": "SPEENPITSMPSEKNSSPIV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser666", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser666" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.675.675", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.678.678", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.683.683", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.667.667", "start_pos": 667, "end_pos": 667, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSFMLSPFRQQFTDNAARSS", "down_seq": "PEENPITSMPSEKNSSPIVD", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser667", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser667" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.675.675", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.678.678", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.683.683", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.675.675", "start_pos": 675, "end_pos": 675, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQQFTDNAARSSSPEENPIT", "down_seq": "MPSEKNSSPIVDKKSSKKSR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser675", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser675" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.678.678", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.683.683", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.678.678", "start_pos": 678, "end_pos": 678, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast.", "journal": "Cell reports", "date": "2021-12-28", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Hu Zehan, Jaquenoud Malika, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FTDNAARSSSPEENPITSMP", "down_seq": "EKNSSPIVDKKSSKKSRSKR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser678", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P39969" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ], "site_lbl": "Ser678" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.675.675", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.683.683", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" }, { "database": "O-GlcNAc Atlas", "id": "P39969", "url": "https://oglcnac.org/atlas/detail/P39969" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P39969", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P39969" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P39969-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.1004.1004", "start_pos": 1004, "end_pos": 1004, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTTIGSNGFSSPFLLASGLL", "down_seq": "PGVARNSSMRGTEKKGKFST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1004" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P39969-1.1012.1012", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.1012.1012", "start_pos": 1012, "end_pos": 1012, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FSSPFLLASGLLSPGVARNS", "down_seq": "MRGTEKKGKFSTEEDYFGDN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1012" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P39969-1.1004.1004", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVVFTQKITVEKAPTLMRAK", "down_seq": "TKRIYSPLTNEDPLLSSTFI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Ser118" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P39969-1.124.124", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSNDREVPTL", "down_seq": "QLNTTVSRDKDVSDTLSPDF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser11" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39969-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KITVEKAPTLMRAKSTKRIY", "down_seq": "PLTNEDPLLSSTFISENDSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser124" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39969-1.118.118", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.143.143", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKRIYSPLTNEDPLLSSTFI", "down_seq": "ENDSNSELPTPQPIETAASI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser139" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.124.124", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.145.145", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.149.149", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YSPLTNEDPLLSSTFISEND", "down_seq": "NSELPTPQPIETAASISRTA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser143" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.124.124", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.145.145", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.149.149", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLTNEDPLLSSTFISENDSN", "down_seq": "ELPTPQPIETAASISRTANG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser145" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39969-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.149.149", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EDPLLSSTFISENDSNSELP", "down_seq": "PQPIETAASISRTANGKIER", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr149" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39969-1.139.139", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.145.145", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSNDREVPTLSQLN", "down_seq": "TVSRDKDVSDTLSPDFDSKG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr15" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSNDREVPTLSQLNT", "down_seq": "VSRDKDVSDTLSPDFDSKGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr16" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39969-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PIETAASISRTANGKIERNL", "down_seq": "LKNTMSDIDNALLEFKDDSI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser172" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P39969-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.191.191", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SISRTANGKIERNLSLKNTM", "down_seq": "DIDNALLEFKDDSIGPPDRF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser178" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39969-1.172.172", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.191.191", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSNDREVPTLSQLNTTV", "down_seq": "RDKDVSDTLSPDFDSKGSAT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser18" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSLKNTMSDIDNALLEFKDD", "down_seq": "IGPPDRFINSGRDEEHSITH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser191" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.172.172", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.208.208", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDDSIGPPDRFINSGRDEEH", "down_seq": "ITHETILSATDGLDVVESNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser208" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39969-1.191.191", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DREVPTLSQLNTTVSRDKDV", "down_seq": "DTLSPDFDSKGSATGRDGGN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser24" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EVPTLSQLNTTVSRDKDVSD", "down_seq": "LSPDFDSKGSATGRDGGNFP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr26" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PTLSQLNTTVSRDKDVSDTL", "down_seq": "PDFDSKGSATGRDGGNFPMY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "NDREVPTLSQLNTTVSRDKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39969-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LNTTVSRDKDVSDTLSPDFD", "down_seq": "KGSATGRDGGNFPMYIAINE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser33" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KEIEKIKEAIRTNGRSLNRA", "down_seq": "KTNNANIYNQLMPPANVDQR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser342" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVSRDKDVSDTLSPDFDSKG", "down_seq": "ATGRDGGNFPMYIAINEYFK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser36" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.16.16", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39969-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.33.33", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HVRKTSQSLEDLPSQQNFIP", "down_seq": "PRNTRNSSASKHRPKSLVFD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr388" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.372.372", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.373.373", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.375.375", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.381.381", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.438.438", "start_pos": 438, "end_pos": 438, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDVQIPQVVEEMAGNENLFV", "down_seq": "PRRAPKPPSYPSPAQPPKSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser438" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P39969-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.450.450", "start_pos": 450, "end_pos": 450, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AGNENLFVSPRRAPKPPSYP", "down_seq": "PAQPPKSPLLNNTRTSPSPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser450" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39969-1.438.438", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSPRRAPKPPSYPSPAQPPK", "down_seq": "PLLNNTRTSPSPAQLYSWQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser457" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.438.438", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.465.465", "start_pos": 465, "end_pos": 465, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PPSYPSPAQPPKSPLLNNTR", "down_seq": "SPSPAQLYSWQSPTLSFSGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr465" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSYPSPAQPPKSPLLNNTRT", "down_seq": "PSPAQLYSWQSPTLSFSGPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser466" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.468.468", "start_pos": 468, "end_pos": 468, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YPSPAQPPKSPLLNNTRTSP", "down_seq": "PAQLYSWQSPTLSFSGPKRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser468" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.473.473", "start_pos": 473, "end_pos": 473, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QPPKSPLLNNTRTSPSPAQL", "down_seq": "SWQSPTLSFSGPKRTSYIDQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Tyr473" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.477.477", "start_pos": 477, "end_pos": 477, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPLLNNTRTSPSPAQLYSWQ", "down_seq": "PTLSFSGPKRTSYIDQYSSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser477" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.481.481", "start_pos": 481, "end_pos": 481, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNTRTSPSPAQLYSWQSPTL", "down_seq": "FSGPKRTSYIDQYSSSDSNF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser481" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.483.483", "start_pos": 483, "end_pos": 483, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRTSPSPAQLYSWQSPTLSF", "down_seq": "GPKRTSYIDQYSSSDSNFNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser483" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.465.465", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39969-1.466.466", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.468.468", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.490.490", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.490.490", "start_pos": 490, "end_pos": 490, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AQLYSWQSPTLSFSGPKRTS", "down_seq": "IDQYSSSDSNFNSRSALPKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr490" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39969-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.481.481", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.483.483", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.488.488", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.489.489", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.495.495", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.496.496", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.497.497", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.519.519", "start_pos": 519, "end_pos": 519, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.", "journal": "Nature biotechnology", "date": "2002-03", "authors": "Ficarro Scott B, McCleland Mark L, Stukenberg P Todd, Burke Daniel J, Ross Mark M, Shabanowitz Jeffrey, Hunt Donald F, White Forest M", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNFNSRSALPKNNQGGGKAL", "down_seq": "PIPSPTRNSVRNEDSEGKLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser519" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.499.499", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.525.525", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 16 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.523.523", "start_pos": 523, "end_pos": 523, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRSALPKNNQGGGKALSPIP", "down_seq": "PTRNSVRNEDSEGKLTSSSK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser523" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.503.503", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.525.525", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.541.541", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 15 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.525.525", "start_pos": 525, "end_pos": 525, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.", "journal": "Nature biotechnology", "date": "2002-03", "authors": "Ficarro Scott B, McCleland Mark L, Stukenberg P Todd, Burke Daniel J, Ross Mark M, Shabanowitz Jeffrey, Hunt Donald F, White Forest M", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SALPKNNQGGGKALSPIPSP", "down_seq": "RNSVRNEDSEGKLTSSSKRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr525" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39969-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.541.541", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PKNNQGGGKALSPIPSPTRN", "down_seq": "VRNEDSEGKLTSSSKRNSVP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser528" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P39969-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.525.525", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.541.541", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.546.546", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.534.534", "start_pos": 534, "end_pos": 534, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGKALSPIPSPTRNSVRNED", "down_seq": "EGKLTSSSKRNSVPYYGYAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser534" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.525.525", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.541.541", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.546.546", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.549.549", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.541.541", "start_pos": 541, "end_pos": 541, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IPSPTRNSVRNEDSEGKLTS", "down_seq": "SKRNSVPYYGYAPESSSDRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser541" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.523.523", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.525.525", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.546.546", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.549.549", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.546.546", "start_pos": 546, "end_pos": 546, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RNSVRNEDSEGKLTSSSKRN", "down_seq": "VPYYGYAPESSSDRKSSCSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser546" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.528.528", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.541.541", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.549.549", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.549.549", "start_pos": 549, "end_pos": 549, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VRNEDSEGKLTSSSKRNSVP", "down_seq": "YGYAPESSSDRKSSCSSHEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr549" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.541.541", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.546.546", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.584.584", "start_pos": 584, "end_pos": 584, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CSSHEEEQFQETMNTFERPT", "down_seq": "SIYADGSTIASISNDKLAHE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser584" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P39969-1.591.591", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.595.595", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.597.597", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.591.591", "start_pos": 591, "end_pos": 591, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QFQETMNTFERPTSSIYADG", "down_seq": "TIASISNDKLAHEKEGKKKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser591" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P39969-1.584.584", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.595.595", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.597.597", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.595.595", "start_pos": 595, "end_pos": 595, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TMNTFERPTSSIYADGSTIA", "down_seq": "ISNDKLAHEKEGKKKPTRHS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser595" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P39969-1.584.584", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.591.591", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.597.597", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.597.597", "start_pos": 597, "end_pos": 597, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTFERPTSSIYADGSTIASI", "down_seq": "NDKLAHEKEGKKKPTRHSSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser597" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P39969-1.584.584", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.591.591", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.595.595", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.616.616", "start_pos": 616, "end_pos": 616, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ISNDKLAHEKEGKKKPTRHS", "down_seq": "SLSSKSKSDSRRNSSLKRSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser616" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.617.617", "start_pos": 617, "end_pos": 617, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNDKLAHEKEGKKKPTRHSS", "down_seq": "LSSKSKSDSRRNSSLKRSSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser617" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.597.597", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.619.619", "start_pos": 619, "end_pos": 619, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DKLAHEKEGKKKPTRHSSSL", "down_seq": "SKSKSDSRRNSSLKRSSSAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser619" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.622.622", "start_pos": 622, "end_pos": 622, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AHEKEGKKKPTRHSSSLSSK", "down_seq": "KSDSRRNSSLKRSSSASRTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser622" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.626.626", "start_pos": 626, "end_pos": 626, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGKKKPTRHSSSLSSKSKSD", "down_seq": "RRNSSLKRSSSASRTSSFKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser626" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.630.630", "start_pos": 630, "end_pos": 630, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPTRHSSSLSSKSKSDSRRN", "down_seq": "SLKRSSSASRTSSFKKSSFM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser630" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.631.631", "start_pos": 631, "end_pos": 631, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PTRHSSSLSSKSKSDSRRNS", "down_seq": "LKRSSSASRTSSFKKSSFML", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser631" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.616.616", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.637.637", "start_pos": 637, "end_pos": 637, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLSSKSKSDSRRNSSLKRSS", "down_seq": "ASRTSSFKKSSFMLSPFRQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser637" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.617.617", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P39969-1.619.619", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.642.642", "start_pos": 642, "end_pos": 642, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKSDSRRNSSLKRSSSASRT", "down_seq": "SFKKSSFMLSPFRQQFTDNA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser642" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P39969-1.622.622", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.643.643", "start_pos": 643, "end_pos": 643, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSDSRRNSSLKRSSSASRTS", "down_seq": "FKKSSFMLSPFRQQFTDNAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser643" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39969-1.626.626", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.647.647", "start_pos": 647, "end_pos": 647, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRNSSLKRSSSASRTSSFKK", "down_seq": "SFMLSPFRQQFTDNAARSSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser647" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39969-1.630.630", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.652.652", "start_pos": 652, "end_pos": 652, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKRSSSASRTSSFKKSSFML", "down_seq": "PFRQQFTDNAARSSSPEENP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ], "site_lbl": "Ser652" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ], "site_lbl": "Ser652" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser652" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P39969-1.637.637", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.659.659", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.659.659", "start_pos": 659, "end_pos": 659, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SRTSSFKKSSFMLSPFRQQF", "down_seq": "DNAARSSSPEENPITSMPSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr659" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P39969-1.642.642", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.643.643", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P39969-1.647.647", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39969-1.652.652", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P39969-1.675.675", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.678.678", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.683.683", "start_pos": 683, "end_pos": 683, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARSSSPEENPITSMPSEKNS", "down_seq": "PIVDKKSSKKSRSKRRSVSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser683" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P39969-1.665.665", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P39969-1.666.666", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P39969-1.667.667", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P39969-1.675.675", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P39969-1.678.678", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.702.702", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.702.702", "start_pos": 702, "end_pos": 702, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSPIVDKKSSKKSRSKRRSV", "down_seq": "AKEAEIFTETVKDDKNKRSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser702" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.683.683", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39969-1.721.721", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.721.721", "start_pos": 721, "end_pos": 721, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSAKEAEIFTETVKDDKNKR", "down_seq": "ASEAIKGETLKGKSLRQMTA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser721" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39969-1.702.702", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P39969-1.723.723", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.723.723", "start_pos": 723, "end_pos": 723, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKEAEIFTETVKDDKNKRSA", "down_seq": "EAIKGETLKGKSLRQMTARP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser723" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P39969-1.721.721", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.901.901", "start_pos": 901, "end_pos": 901, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ALIKTTIDIDTSVPIISSYT", "down_seq": "PTVSLSKAQEMLAEAREETK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr901" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39969-1.961.961", "start_pos": 961, "end_pos": 961, "uniprot_canonical_ac": "P39969-1", "length": 1040, "uniprot_id": "BOI2_YEAST", "protein_name": "BEM1-interacting protein 2", "refseq_ac": "NP_011039", "refseq_name": "Boi2p", "gene_name": "BOI2", "gene_names_uniprotkb": "BOI2; BEB1", "gene_names_refseq": "BEB1; BOI2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P39969", "url": "https://www.uniprot.org/uniprotkb/P39969" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQQLQQQQHDNNQGQADRTI", "down_seq": "ASTQRTSDEDNTISTPNLSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000916", "url": "https://www.yeastgenome.org/locus/S000000916" }, { "database": "iPTMnet", "id": "P39969", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P39969" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser961" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1004", "end_pos": "1004" }, { "start_pos": "1012", "end_pos": "1012" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "591", "end_pos": "591" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "616", "end_pos": "616" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "647", "end_pos": "647" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "666", "end_pos": "666" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "721", "end_pos": "721" }, { "start_pos": "723", "end_pos": "723" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "961", "end_pos": "961" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ENGLAALVESAQQAAAEYEG", "down_seq": "PSNDADVRDDELDVIDYNID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr126" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40010-1.128.128", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLAALVESAQQAAAEYEGTP", "down_seq": "NDADVRDDELDVIDYNIDFY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Ser128" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40010-1.126.126", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DELDVIDYNIDFYGEDVEGE", "down_seq": "ELEKSRKAYDKIFKSVIDAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser156" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A proteome-wide analysis of kinase-substrate network in the DNA damage response.", "journal": "The Journal of biological chemistry", "date": "2010-04-23", "authors": "Chen Sheng-hong, Albuquerque Claudio P, Liang Jason, Suhandynata Raymond T, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKSSFPTIPLRASSGAVNGT", "down_seq": "FNRKLSQTTTASALLESLKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" }, { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser250" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P40010-1.256.256", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TIPLRASSGAVNGTSFNRKL", "down_seq": "QTTTASALLESLKTYSNNSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser256" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40010-1.250.250", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TASALLESLKTYSNNSNLKR", "down_seq": "IVVGVIGYPNVGKSSVINAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser280" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.320.320", "start_pos": 320, "end_pos": 320, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLARRGGQSKACPVGNEAGV", "down_seq": "TSLREIKIDNKLKILDSPGI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr320" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40010-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40010-1.322.322", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40010-1.337.337", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LARRGGQSKACPVGNEAGVT", "down_seq": "SLREIKIDNKLKILDSPGIC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" } ], "site_lbl": "Thr321" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40010-1.320.320", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40010-1.322.322", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40010-1.337.337", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.322.322", "start_pos": 322, "end_pos": 322, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARRGGQSKACPVGNEAGVTT", "down_seq": "LREIKIDNKLKILDSPGICF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser322" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40010-1.320.320", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40010-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40010-1.337.337", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.337.337", "start_pos": 337, "end_pos": 337, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AGVTTSLREIKIDNKLKILD", "down_seq": "PGICFPSENKKRSKVEHEAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser337" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40010-1.320.320", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40010-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40010-1.322.322", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GLSVLNDWRDGKILGWVLPN", "down_seq": "SAAASQQDKQNLSTINTGTK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr457" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40010-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40010-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40010-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40010-1.471.471", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSVLNDWRDGKILGWVLPNT", "down_seq": "AAASQQDKQNLSTINTGTKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser458" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40010-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40010-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40010-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40010-1.471.471", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NDWRDGKILGWVLPNTSAAA", "down_seq": "QQDKQNLSTINTGTKQAPIA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser462" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40010-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40010-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40010-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40010-1.471.471", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.470.470", "start_pos": 470, "end_pos": 470, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGWVLPNTSAAASQQDKQNL", "down_seq": "TINTGTKQAPIAANESTIVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser470" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40010-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40010-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40010-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40010-1.471.471", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40010-1.486.486", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.471.471", "start_pos": 471, "end_pos": 471, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GWVLPNTSAAASQQDKQNLS", "down_seq": "INTGTKQAPIAANESTIVSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr471" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40010-1.457.457", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40010-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40010-1.462.462", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40010-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40010-1.486.486", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.486.486", "start_pos": 486, "end_pos": 486, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KQNLSTINTGTKQAPIAANE", "down_seq": "TIVSEWSKEFDLDGLFSSLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser486" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40010-1.470.470", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40010-1.471.471", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40010-1.504.504", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.504.504", "start_pos": 504, "end_pos": 504, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NESTIVSEWSKEFDLDGLFS", "down_seq": "LDKAIDASKDQDTMME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser504" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40010-1.486.486", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40010-1.512.512", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40010-1.517.517", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.512.512", "start_pos": 512, "end_pos": 512, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WSKEFDLDGLFSSLDKAIDA", "down_seq": "KDQDTMME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser512" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40010-1.504.504", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40010-1.517.517", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40010-1.517.517", "start_pos": 517, "end_pos": 517, "uniprot_canonical_ac": "P40010-1", "length": 520, "uniprot_id": "NUG1_YEAST", "protein_name": "Nuclear GTP-binding protein NUG1", "refseq_ac": "NP_010921", "refseq_name": "RNA-binding GTPase NUG1", "gene_name": "NUG1", "gene_names_uniprotkb": "NUG1", "gene_names_refseq": "NUG1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40010", "url": "https://www.uniprot.org/uniprotkb/P40010" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DLDGLFSSLDKAIDASKDQD", "down_seq": "MME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000808", "url": "https://www.yeastgenome.org/locus/S000000808" }, { "database": "iPTMnet", "id": "P40010", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40010" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr517" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "517", "end_pos": "517" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40010-1.504.504", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40010-1.512.512", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P80667-1.10.13", "start_pos": 10, "end_pos": 13, "uniprot_canonical_ac": "P80667-1", "length": 386, "uniprot_id": "PEX13_YEAST", "protein_name": "Peroxisomal membrane protein PEX13", "refseq_ac": "NP_013292", "refseq_name": "peroxin PEX13", "gene_name": "PEX13", "gene_names_uniprotkb": "PEX13; L9470.1; PAS20", "gene_names_refseq": "PAS20; PEX13", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P80667", "url": "https://www.uniprot.org/uniprotkb/P80667" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "PEX39 facilitates the peroxisomal import of PTS2-containing proteins.", "journal": "Nature cell biology", "date": "2025-08", "authors": "Chen Walter W, Rodrigues Tony A, Wendscheck Daniel, Pedrosa Ana G, Yang Chendong, Francisco T\u00e2nia, M\u00f6cklinghoff Till, Zografakis Alexandros, Nunes-Silva Bernardo, Avraham Reut E, Silva Ana R, Ferreira Maria J, Das Hirak, Koster Janet, Neuwirth Simone, Bender Julian, Oeljeklaus Silke, Sondhi Varun, Gatsogiannis Christos, Schuldiner Maya, Zalckvar Einat, Hofmann Kay, Waterham Hans R, DeBerardinis Ralph J, Azevedo Jorge E, Warscheid Bettina", "evidence": [ { "database": "UniProtKB", "id": "P80667", "url": "https://www.uniprot.org/uniprotkb/P80667" } ], "reference": [ { "type": "PubMed", "id": "40739340", "url": "https://glygen.org/publication/PubMed/40739340" } ] } ], "crossref": [ { "id": "P80667", "url": "https://www.uniprot.org/uniprotkb/P80667", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40739340", "url": "https://glygen.org/publication/PubMed/40739340", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "KPWE", "start_aa": "K", "up_seq": "MSSTAVPRP", "down_seq": "TSASLEEPQRNAQSLSAMMT", "mutagenesis": [ { "sequence_org": "KPWE", "sequence_mut": "AAAA", "comment": "Leads to PEX7 being stalled at the peroxisomal membrane. Decreases growth on oleic acid carbon source.", "evidence": [ { "database": "UniProtKB", "id": "P80667", "url": "https://www.uniprot.org/uniprotkb/P80667" }, { "database": "PubMed", "id": "40739340", "url": "https://glygen.org/publication/PubMed/40739340" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "13" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "246", "end_pos": "246" }, { "start_pos": "251", "end_pos": "251" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P80667-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P80667-1", "length": 386, "uniprot_id": "PEX13_YEAST", "protein_name": "Peroxisomal membrane protein PEX13", "refseq_ac": "NP_013292", "refseq_name": "peroxin PEX13", "gene_name": "PEX13", "gene_names_uniprotkb": "PEX13; L9470.1; PAS20", "gene_names_refseq": "PAS20; PEX13", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P80667", "url": "https://www.uniprot.org/uniprotkb/P80667" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P80667", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P80667" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004181", "url": "https://www.yeastgenome.org/locus/S000004181", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P80667", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P80667", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FAESEGSKNKLIEDFQKFND", "down_seq": "GTINSNEKATRRKISWKPLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004181", "url": "https://www.yeastgenome.org/locus/S000004181" }, { "database": "iPTMnet", "id": "P80667", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P80667" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser246" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "13" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "246", "end_pos": "246" }, { "start_pos": "251", "end_pos": "251" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P80667-1.251.251", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P80667-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "P80667-1", "length": 386, "uniprot_id": "PEX13_YEAST", "protein_name": "Peroxisomal membrane protein PEX13", "refseq_ac": "NP_013292", "refseq_name": "peroxin PEX13", "gene_name": "PEX13", "gene_names_uniprotkb": "PEX13; L9470.1; PAS20", "gene_names_refseq": "PAS20; PEX13", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P80667", "url": "https://www.uniprot.org/uniprotkb/P80667" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P80667", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P80667" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004181", "url": "https://www.yeastgenome.org/locus/S000004181", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P80667", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P80667", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSKNKLIEDFQKFNDSGTIN", "down_seq": "NEKATRRKISWKPLLFFLMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004181", "url": "https://www.yeastgenome.org/locus/S000004181" }, { "database": "iPTMnet", "id": "P80667", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P80667" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser251" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "13" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "246", "end_pos": "246" }, { "start_pos": "251", "end_pos": "251" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P80667-1.246.246", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40014-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P40014-1", "length": 221, "uniprot_id": "SPC25_YEAST", "protein_name": "Kinetochore protein SPC25", "refseq_ac": "NP_010934", "refseq_name": "kinetochore-associated Ndc80 complex subunit SPC25", "gene_name": "SPC25", "gene_names_uniprotkb": "SPC25", "gene_names_refseq": "SPC25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40014", "url": "https://www.uniprot.org/uniprotkb/P40014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000820", "url": "https://www.yeastgenome.org/locus/S000000820", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTREQWRSYHERESELSRRQ", "down_seq": "TLAAQSRELDSLLQQRGKEC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000820", "url": "https://www.yeastgenome.org/locus/S000000820" }, { "database": "iPTMnet", "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser100" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40014-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P40014-1", "length": 221, "uniprot_id": "SPC25_YEAST", "protein_name": "Kinetochore protein SPC25", "refseq_ac": "NP_010934", "refseq_name": "kinetochore-associated Ndc80 complex subunit SPC25", "gene_name": "SPC25", "gene_names_uniprotkb": "SPC25", "gene_names_refseq": "SPC25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40014", "url": "https://www.uniprot.org/uniprotkb/P40014" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000820", "url": "https://www.yeastgenome.org/locus/S000000820", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MASIDAF", "down_seq": "DLERRMDGFQKDVAQVLARQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000820", "url": "https://www.yeastgenome.org/locus/S000000820" }, { "database": "iPTMnet", "id": "P40014", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40014" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser8" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VHNIDDISLNFEATSTPPAP", "down_seq": "SAPSIPVEHSNPCTSIEIPK", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr506", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40020-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDSPLKIVFPKSGNETERRM", "down_seq": "TSSLLMNSHGHLVDMHSKIL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser102" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40020-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40020-1.105.105", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLKIVFPKSGNETERRMSTS", "down_seq": "LLMNSHGHLVDMHSKILVDV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser105" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40020-1.102.102", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRSDVRSNTSSSGKEPNHSR", "down_seq": "KSLQSIIVDTMNTYRATEVE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser167" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40020-1.169.169", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40020-1.172.172", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SDVRSNTSSSGKEPNHSRSK", "down_seq": "LQSIIVDTMNTYRATEVETS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser169" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40020-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40020-1.172.172", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSNTSSSGKEPNHSRSKSLQ", "down_seq": "IIVDTMNTYRATEVETSINE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser172" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40020-1.167.167", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40020-1.169.169", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TSNISQVSPLNLSFDRPPPL", "down_seq": "PEKNLYLTPESPLNRYHLPV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr214" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P40020-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40020-1.225.225", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLNLSFDRPPPLTPEKNLYL", "down_seq": "PESPLNRYHLPVPLEISLPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr222" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40020-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40020-1.225.225", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSFDRPPPLTPEKNLYLTPE", "down_seq": "PLNRYHLPVPLEISLPPYLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser225" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40020-1.214.214", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40020-1.222.222", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40020-1.245.245", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPLNRYHLPVPLEISLPPYL", "down_seq": "PQNKDKKRSSLVYDGDGYSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser245" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40020-1.225.225", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSLVYDGDGYSQFQEGNTSS", "down_seq": "TESSLEQPSSSYSDEDDSIP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser274" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "LPVTPVKSKVCSTLSIQHEM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40020-1.6.6", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KTDRECEEKNTEKNVSLKIL", "down_seq": "TPNKLIDIPDLEHMKSPPST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser359" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40020-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40020-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40020-1.378.378", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TDRECEEKNTEKNVSLKILS", "down_seq": "PNKLIDIPDLEHMKSPPSTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr360" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40020-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40020-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40020-1.378.378", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKILSTPNKLIDIPDLEHMK", "down_seq": "PPSTGLNGTLKFFQQFEPSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser375" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser375" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser375" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40020-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40020-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40020-1.378.378", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40020-1.394.394", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSTPNKLIDIPDLEHMKSPP", "down_seq": "TGLNGTLKFFQQFEPSEEPT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser378" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40020-1.359.359", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P40020-1.360.360", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40020-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40020-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40020-1.398.398", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.394.394", "start_pos": 394, "end_pos": 394, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSPPSTGLNGTLKFFQQFEP", "down_seq": "EEPTSPTRQVNPESLDKLDM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Ser394" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40020-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40020-1.378.378", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40020-1.398.398", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40020-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40020-1.408.408", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.398.398", "start_pos": 398, "end_pos": 398, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "STGLNGTLKFFQQFEPSEEP", "down_seq": "SPTRQVNPESLDKLDMSFKF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr398" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40020-1.378.378", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40020-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40020-1.399.399", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40020-1.408.408", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TGLNGTLKFFQQFEPSEEPT", "down_seq": "PTRQVNPESLDKLDMSFKFP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser399" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40020-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40020-1.398.398", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40020-1.408.408", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.408.408", "start_pos": 408, "end_pos": 408, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FQQFEPSEEPTSPTRQVNPE", "down_seq": "LDKLDMSFKFPSSTTNNNVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser408" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40020-1.394.394", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40020-1.398.398", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40020-1.399.399", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.436.436", "start_pos": 436, "end_pos": 436, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FKFPSSTTNNNVDKVHENRN", "down_seq": "GDTNNEDFLKVDTSPVNQSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser436" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P40020-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40020-1.449.449", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40020-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40020-1.455.455", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSSTTNNNVDKVHENRNSGD", "down_seq": "NNEDFLKVDTSPVNQSFESR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr439" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40020-1.436.436", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40020-1.449.449", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40020-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40020-1.455.455", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40020-1.458.458", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KVHENRNSGDTNNEDFLKVD", "down_seq": "SPVNQSFESRRQMLIDLQKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr449" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40020-1.436.436", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40020-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40020-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40020-1.455.455", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40020-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40020-1.469.469", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.450.450", "start_pos": 450, "end_pos": 450, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VHENRNSGDTNNEDFLKVDT", "down_seq": "PVNQSFESRRQMLIDLQKSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser450" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40020-1.436.436", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40020-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40020-1.449.449", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40020-1.455.455", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40020-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40020-1.469.469", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.455.455", "start_pos": 455, "end_pos": 455, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSGDTNNEDFLKVDTSPVNQ", "down_seq": "FESRRQMLIDLQKSPTNNNP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser455" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40020-1.436.436", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40020-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40020-1.449.449", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40020-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40020-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40020-1.469.469", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DTNNEDFLKVDTSPVNQSFE", "down_seq": "RRQMLIDLQKSPTNNNPRIH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser458" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40020-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40020-1.449.449", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40020-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40020-1.455.455", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40020-1.469.469", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.469.469", "start_pos": 469, "end_pos": 469, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSPVNQSFESRRQMLIDLQK", "down_seq": "PTNNNPRIHKHRRSRSVHNI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser469" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40020-1.449.449", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P40020-1.450.450", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P40020-1.455.455", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40020-1.458.458", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40020-1.485.485", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.485.485", "start_pos": 485, "end_pos": 485, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLQKSPTNNNPRIHKHRRSR", "down_seq": "VHNIDDISLNFEATSTPPAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser485" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40020-1.469.469", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.533.533", "start_pos": 533, "end_pos": 533, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VEHSNPCTSIEIPKRSPLRF", "down_seq": "SSPKTSDIPPEAQSPKNGSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Thr533" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40020-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40020-1.535.535", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40020-1.547.547", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.534.534", "start_pos": 534, "end_pos": 534, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EHSNPCTSIEIPKRSPLRFT", "down_seq": "SPKTSDIPPEAQSPKNGSFL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Ser534" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40020-1.533.533", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40020-1.535.535", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40020-1.547.547", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HSNPCTSIEIPKRSPLRFTS", "down_seq": "PKTSDIPPEAQSPKNGSFLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Ser535" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40020-1.533.533", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40020-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40020-1.547.547", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.547.547", "start_pos": 547, "end_pos": 547, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSPLRFTSSPKTSDIPPEAQ", "down_seq": "PKNGSFLQEISVPSIQIIPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser547" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40020-1.533.533", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40020-1.534.534", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40020-1.535.535", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.634.634", "start_pos": 634, "end_pos": 634, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PFKPLSSFNSFGQEIQNKEP", "down_seq": "PLNQTPTDLIGKQRNCVNPH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr634" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40020-1.639.639", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.639.639", "start_pos": 639, "end_pos": 639, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSFNSFGQEIQNKEPTPLNQ", "down_seq": "PTDLIGKQRNCVNPHSIPFS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr639" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40020-1.634.634", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IESVAIPRQRSSKNKKPHEH", "down_seq": "QSQVRFSIPDPNEISQDSPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr66" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P40020-1.73.73", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40020-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40020-1.84.84", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSLPV", "down_seq": "PVKSKVCSTLSIQHEMDHDQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr6" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40020-1.2.2", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQRSSKNKKPHEHTQSQVRF", "down_seq": "IPDPNEISQDSPLKIVFPKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser73" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40020-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40020-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40020-1.84.84", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPHEHTQSQVRFSIPDPNEI", "down_seq": "QDSPLKIVFPKSGNETERRM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser81" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40020-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40020-1.73.73", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40020-1.84.84", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40020-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P40020-1", "length": 876, "uniprot_id": "FIR1_YEAST", "protein_name": "Factor interacting with REF2", "refseq_ac": "NP_010949", "refseq_name": "Fir1p", "gene_name": "FIR1", "gene_names_uniprotkb": "FIR1; PIP1", "gene_names_refseq": "FIR1; PIP1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40020", "url": "https://www.uniprot.org/uniprotkb/P40020" }, { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EHTQSQVRFSIPDPNEISQD", "down_seq": "PLKIVFPKSGNETERRMSTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40020", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40020" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000834", "url": "https://www.yeastgenome.org/locus/S000000834" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser84" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "506", "end_pos": "506" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "639", "end_pos": "639" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40020-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40020-1.73.73", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40020-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40020-1.102.102", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LVLSTSFISTKRLENSAPSP", "down_seq": "SPLMARRTRSTMTKALLNLK", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr86", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr86" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.1061.1061", "start_pos": 1061, "end_pos": 1061, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRPYGFQLLNEINFVKEERD", "down_seq": "WLSKKNIEYVHIVEEFLKKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1061" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSIPHSAKQS", "down_seq": "PLSSRRRSVTNTTPLLTPRH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser11" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40061-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.1310.1310", "start_pos": 1310, "end_pos": 1310, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLNEKIITNKYDNDITSQTI", "down_seq": "VSGENSSLFANEGLSSPYVT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr1310" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P40061-1.1326.1326", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.1326.1326", "start_pos": 1326, "end_pos": 1326, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQTITVSGENSSLFANEGLS", "down_seq": "PYVTQYRNDDDSIESKVLHI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1326" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40061-1.1310.1310", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKKDDIEHLRDSTISDIYSG", "down_seq": "YSTNHLQKHSMRIRANTQLR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" } ], "site_lbl": "Ser141" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLQKHSMRIRANTQLREIDN", "down_seq": "IKRVEKHIFDLKQQFDKKRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser166" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EKHIFDLKQQFDKKRQRSLT", "down_seq": "SSSIKADVGSIRNDDGQNND", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr191" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40061-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.201.201", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KHIFDLKQQFDKKRQRSLTT", "down_seq": "SSIKADVGSIRNDDGQNNDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser192" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40061-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.201.201", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HIFDLKQQFDKKRQRSLTTS", "down_seq": "SIKADVGSIRNDDGQNNDSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser193" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40061-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.201.201", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IFDLKQQFDKKRQRSLTTSS", "down_seq": "IKADVGSIRNDDGQNNDSEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser194" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40061-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40061-1.201.201", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSIPHSAKQSSPLSSRRR", "down_seq": "VTNTTPLLTPRHSRDNSSTQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser19" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FDKKRQRSLTTSSSIKADVG", "down_seq": "IRNDDGQNNDSEELGDHDSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser201" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40061-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40061-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40061-1.194.194", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSIPHSAKQSSPLSSRRRSV", "down_seq": "NTTPLLTPRHSRDNSSTQIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr21" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40061-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40061-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ELGDHDSLTDQVTLDDEYLT", "down_seq": "PTSGTERNSQQNLNRNSTVN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr234" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P40061-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DHDSLTDQVTLDDEYLTTPT", "down_seq": "GTERNSQQNLNRNSTVNSRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser237" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40061-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40061-1.255.255", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IPHSAKQSSPLSSRRRSVTN", "down_seq": "TPLLTPRHSRDNSSTQISSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr23" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40061-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DQVTLDDEYLTTPTSGTERN", "down_seq": "QQNLNRNSTVNSRNNENHST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40061-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40061-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40061-1.262.262", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40061-1.263.263", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PHSAKQSSPLSSRRRSVTNT", "down_seq": "PLLTPRHSRDNSSTQISSAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr24" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40061-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YLTTPTSGTERNSQQNLNRN", "down_seq": "TVNSRNNENHSTLSIPDLDG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser251" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P40061-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40061-1.262.262", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40061-1.263.263", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40061-1.265.265", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PTSGTERNSQQNLNRNSTVN", "down_seq": "RNNENHSTLSIPDLDGSNKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser255" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40061-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40061-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40061-1.262.262", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.263.263", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.265.265", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSQQNLNRNSTVNSRNNENH", "down_seq": "TLSIPDLDGSNKVNLTGDTE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser262" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40061-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40061-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.263.263", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.265.265", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SQQNLNRNSTVNSRNNENHS", "down_seq": "LSIPDLDGSNKVNLTGDTEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr263" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40061-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.262.262", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.265.265", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNLNRNSTVNSRNNENHSTL", "down_seq": "IPDLDGSNKVNLTGDTEKDL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser265" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40061-1.251.251", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40061-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.262.262", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.263.263", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KQSSPLSSRRRSVTNTTPLL", "down_seq": "PRHSRDNSSTQISSAKNITS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Thr28" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Thr28" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "IPHSAKQSSPLSSRRRSVTN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P40061-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLSSRRRSVTNTTPLLTPRH", "down_seq": "RDNSSTQISSAKNITSSSPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser32" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRRSVTNTTPLLTPRHSRDN", "down_seq": "STQISSAKNITSSSPSTITN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser36" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNTTPLLTPRHSRDNSSTQI", "down_seq": "SAKNITSSSPSTITNESSKR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser41" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40061-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTTPLLTPRHSRDNSSTQIS", "down_seq": "AKNITSSSPSTITNESSKRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser42" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40061-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P40061-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTPRHSRDNSSTQISSAKNI", "down_seq": "SSSPSTITNESSKRNKQNLV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Thr47" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPRHSRDNSSTQISSAKNIT", "down_seq": "SSPSTITNESSKRNKQNLVL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser48" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40061-1.28.28", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PRHSRDNSSTQISSAKNITS", "down_seq": "SPSTITNESSKRNKQNLVLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser49" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RHSRDNSSTQISSAKNITSS", "down_seq": "PSTITNESSKRNKQNLVLST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser50" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRDNSSTQISSAKNITSSSP", "down_seq": "TITNESSKRNKQNLVLSTSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser52" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40061-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RDNSSTQISSAKNITSSSPS", "down_seq": "ITNESSKRNKQNLVLSTSFI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr53" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TQISSAKNITSSSPSTITNE", "down_seq": "SKRNKQNLVLSTSFISTKRL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser58" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40061-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40061-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40061-1.47.47", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40061-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40061-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40061-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSTITNESSKRNKQNLVLST", "down_seq": "FISTKRLENSAPSPTSPLMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" } ], "site_lbl": "Ser71" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40061-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P40061-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40061-1.58.58", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40061-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40061-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40061-1.86.86", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40061-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RNKQNLVLSTSFISTKRLEN", "down_seq": "APSPTSPLMARRTRSTMTKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser81" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40061-1.86.86", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40061-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNLVLSTSFISTKRLENSAP", "down_seq": "PTSPLMARRTRSTMTKALLN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser84" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40061-1.86.86", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40061-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VLSTSFISTKRLENSAPSPT", "down_seq": "PLMARRTRSTMTKALLNLKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser87" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40061-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40061-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40061-1.84.84", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40061-1.86.86", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40061-1.986.986", "start_pos": 986, "end_pos": 986, "uniprot_canonical_ac": "P40061-1", "length": 1430, "uniprot_id": "TSC11_YEAST", "protein_name": "Target of rapamycin complex 2 subunit TSC11", "refseq_ac": "NP_011018", "refseq_name": "TORC2 complex subunit TSC11", "gene_name": "TSC11", "gene_names_uniprotkb": "TSC11; AVO3", "gene_names_refseq": "AVO3; TSC11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40061", "url": "https://www.uniprot.org/uniprotkb/P40061" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SDLKLKANKVKLQQFKMEML", "down_seq": "RQLYDLSPSVVAVADQALYE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000895", "url": "https://www.yeastgenome.org/locus/S000000895" }, { "database": "iPTMnet", "id": "P40061", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40061" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr986" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "86", "end_pos": "86" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1061", "end_pos": "1061" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1310", "end_pos": "1310" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "986", "end_pos": "986" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VDLTADAIDLDAEEQQVLQI", "down_seq": "DDDFQEETKEAPKEYGAAKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser183" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SVRQNDEEEENEVSRTQNIV", "down_seq": "DNRHDSPEAVVEIIGERALE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr44" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P40072-1.50.50", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEEENEVSRTQNIVTDNRHD", "down_seq": "PEAVVEIIGERALENTSEED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser50" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40072-1.44.44", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40072-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40072-1.67.67", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NRHDSPEAVVEIIGERALEN", "down_seq": "SEEDGDDDLSLFRALEEDPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr66" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40072-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40072-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40072-1.76.76", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RHDSPEAVVEIIGERALENT", "down_seq": "EEDGDDDLSLFRALEEDPGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser67" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40072-1.50.50", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40072-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40072-1.76.76", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40072-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIIGERALENTSEEDGDDDL", "down_seq": "LFRALEEDPGSDHNTSNNDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser76" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40072-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40072-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40072-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40072-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40072-1.92.92", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEEDGDDDLSLFRALEEDPG", "down_seq": "DHNTSNNDSGNHDRETMHTE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser87" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40072-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40072-1.76.76", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40072-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40072-1.92.92", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GDDDLSLFRALEEDPGSDHN", "down_seq": "SNNDSGNHDRETMHTEEPEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr91" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40072-1.76.76", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40072-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40072-1.92.92", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40072-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P40072-1", "length": 274, "uniprot_id": "SLX8_YEAST", "protein_name": "E3 ubiquitin-protein ligase complex SLX5-SLX8 subunit SLX8", "refseq_ac": "NP_011041", "refseq_name": "SUMO-targeted ubiquitin ligase complex subunit SLX8", "gene_name": "SLX8", "gene_names_uniprotkb": "SLX8", "gene_names_refseq": "SLX8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40072", "url": "https://www.uniprot.org/uniprotkb/P40072" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DDDLSLFRALEEDPGSDHNT", "down_seq": "NNDSGNHDRETMHTEEPEAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000918", "url": "https://www.yeastgenome.org/locus/S000000918" }, { "database": "iPTMnet", "id": "P40072", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40072" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser92" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "183", "end_pos": "183" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40072-1.76.76", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40072-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40072-1.91.91", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MNMNMNMNMNMNMNMNMNMN", "down_seq": "HTTSDHNAHPQYRCRPNPSR", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn123", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DSPSSSSLPLTQTGGPSSAD", "down_seq": "DSIATGTNNRSPQQTKAADA", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn236", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NKLPLTASVPSSLSTTTDAA", "down_seq": "SSFINSSISSPAPSSSSSSS", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn437", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40095-1.432.432", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40095-1.438.438", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40095-1.442.442", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40095-1.444.444", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TASVPSSLSTTTDAANSSFI", "down_seq": "SSISSPAPSSSSSSSLVSRG", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn442", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40095-1.432.432", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40095-1.437.437", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40095-1.438.438", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40095-1.444.444", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.472.472", "start_pos": 472, "end_pos": 472, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSSSSSLVSRGPMQSISSSP", "down_seq": "PAPSSGSSKSKNAVKSLRFA", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr472", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.498.498", "start_pos": 498, "end_pos": 498, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GSSKSKNAVKSLRFADEIYV", "down_seq": "DTWSAADYCRCDNTFLNNFF", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn498", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NNFFKGKSQDITNPSTFVGN", "down_seq": "LSSTKNISNIEIKMEVNEFK", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn535", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P40095-1.541.541", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40095-1.543.543", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.541.541", "start_pos": 541, "end_pos": 541, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KSQDITNPSTFVGNNLSSTK", "down_seq": "ISNIEIKMEVNEFKRKEMRV", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn541", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40095-1.535.535", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40095-1.543.543", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IDLFYIPDATVSRRHSTLVA", "down_seq": "RSDNNGNGAPMRQYNKPNFA", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn63", "evidence": [ { "id": "P40095", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P40095#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P40095-1.77.77", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40095-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLQQGSSSRR", "down_seq": "LHGNDFHTLTSPSRRDSLSI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" } ], "site_lbl": "Ser11" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P40095-1.28.28", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RHSLMTIPEKYSGSRYSLRS", "down_seq": "PPTYSNPRVRKELTPFQLQR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" }, { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser164" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNRSPQQTKAADANQKSESE", "down_seq": "PKAIRSNSKKISRFFRKIWS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" }, { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser264" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRRSLHGNDFHTLTSPSRRD", "down_seq": "LSIPRAVDARSASTIDLFYI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" } ], "site_lbl": "Ser28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40095-1.11.11", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.368.368", "start_pos": 368, "end_pos": 368, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQELTALGDNNRIPVLPPPR", "down_seq": "PNRPTLSDKRTTKLYYCSQD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" }, { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser368" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.390.390", "start_pos": 390, "end_pos": 390, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NRPTLSDKRTTKLYYCSQDS", "down_seq": "NEDIAPEEKSTVFLKRLQDE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" }, { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser390" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "STVYLNKLPLTASVPSSLST", "down_seq": "TDAANSSFINSSISSPAPSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" } ], "site_lbl": "Thr432" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40095-1.437.437", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40095-1.438.438", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40095-1.442.442", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40095-1.444.444", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.438.438", "start_pos": 438, "end_pos": 438, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLPLTASVPSSLSTTTDAAN", "down_seq": "SFINSSISSPAPSSSSSSSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" } ], "site_lbl": "Ser438" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40095-1.432.432", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40095-1.437.437", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40095-1.442.442", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40095-1.444.444", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.444.444", "start_pos": 444, "end_pos": 444, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVPSSLSTTTDAANSSFINS", "down_seq": "ISSPAPSSSSSSSLVSRGPM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" } ], "site_lbl": "Ser444" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40095-1.432.432", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40095-1.437.437", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40095-1.438.438", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40095-1.442.442", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.543.543", "start_pos": 543, "end_pos": 543, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDITNPSTFVGNNLSSTKNI", "down_seq": "NIEIKMEVNEFKRKEMRVHQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" }, { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser543" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40095-1.535.535", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40095-1.541.541", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40095-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P40095-1", "length": 573, "uniprot_id": "YEY8_YEAST", "protein_name": "Uncharacterized protein YER158C", "refseq_ac": "NP_011085", "refseq_name": "uncharacterized protein", "gene_name": "", "gene_names_uniprotkb": "", "gene_names_refseq": "", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40095", "url": "https://www.uniprot.org/uniprotkb/P40095" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HSTLVANRSDNNGNGAPMRQ", "down_seq": "NKPNFASSSTSSLPSTRNRP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000000960", "url": "https://www.yeastgenome.org/locus/S000000960" }, { "database": "iPTMnet", "id": "P40095", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40095" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Tyr77" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "77", "end_pos": "77" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40095-1.63.63", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40302-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P40302-1", "length": 234, "uniprot_id": "PSA6_YEAST", "protein_name": "Proteasome subunit alpha type-6", "refseq_ac": "NP_014045", "refseq_name": "proteasome core particle subunit alpha 6", "gene_name": "PRE5", "gene_names_uniprotkb": "PRE5; YM9924.06", "gene_names_refseq": "PRE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MFRNNYDGD", "down_seq": "VTFSPTGRLFQVEYALEAIK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Thr10" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40302-1.14.14", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40302-1.16.16", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40302-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P40302-1", "length": 234, "uniprot_id": "PSA6_YEAST", "protein_name": "Proteasome subunit alpha type-6", "refseq_ac": "NP_014045", "refseq_name": "proteasome core particle subunit alpha 6", "gene_name": "PRE5", "gene_names_uniprotkb": "PRE5; YM9924.06", "gene_names_refseq": "PRE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MFRNNYDGDTVTF", "down_seq": "PTGRLFQVEYALEAIKQGSV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser14" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40302-1.10.10", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40302-1.16.16", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40302-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P40302-1", "length": 234, "uniprot_id": "PSA6_YEAST", "protein_name": "Proteasome subunit alpha type-6", "refseq_ac": "NP_014045", "refseq_name": "proteasome core particle subunit alpha 6", "gene_name": "PRE5", "gene_names_uniprotkb": "PRE5; YM9924.06", "gene_names_refseq": "PRE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] } ], "crossref": [ { "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MFRNNYDGDTVTFSP", "down_seq": "GRLFQVEYALEAIKQGSVTV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ], "site_lbl": "Thr16" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40302-1.10.10", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40302-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40302-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "P40302-1", "length": 234, "uniprot_id": "PSA6_YEAST", "protein_name": "Proteasome subunit alpha type-6", "refseq_ac": "NP_014045", "refseq_name": "proteasome core particle subunit alpha 6", "gene_name": "PRE5", "gene_names_uniprotkb": "PRE5; YM9924.06", "gene_names_refseq": "PRE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TFIKIDGNPDELIKAGVEAI", "down_seq": "QSLRDESLTVDNLSIAIVGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser198" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40302-1.200.200", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40302-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P40302-1", "length": 234, "uniprot_id": "PSA6_YEAST", "protein_name": "Proteasome subunit alpha type-6", "refseq_ac": "NP_014045", "refseq_name": "proteasome core particle subunit alpha 6", "gene_name": "PRE5", "gene_names_uniprotkb": "PRE5; YM9924.06", "gene_names_refseq": "PRE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40302", "url": "https://www.uniprot.org/uniprotkb/P40302" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IKIDGNPDELIKAGVEAISQ", "down_seq": "LRDESLTVDNLSIAIVGKDT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004931", "url": "https://www.yeastgenome.org/locus/S000004931" }, { "database": "iPTMnet", "id": "P40302", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40302" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser200" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40302-1.198.198", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cloning and expression of a yeast gene encoding a protein with ATPase activity and high identity to the subunit 4 of the human 26 S protease.", "journal": "The Journal of biological chemistry", "date": "1995-04-21", "authors": "Lucero H A, Chojnicki E W, Mandiyan S, Nelson H, Nelson N", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "reference": [ { "type": "PubMed", "id": "7721833", "url": "https://glygen.org/publication/PubMed/7721833" } ] } ], "crossref": [ { "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7721833", "url": "https://glygen.org/publication/PubMed/7721833", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EEMGIKPPKGVILYGAPGTG", "down_seq": "TLLAKAVANQTSATFLRIVG", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "Q", "comment": "73% loss of ATPase activity.", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "PubMed", "id": "7721833", "url": "https://glygen.org/publication/PubMed/7721833" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P40327-1.241.241", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IVGVLQDDADPMVSVMKMDK", "down_seq": "PTESYSDIGGLESQIQEIKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser176" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40327-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40327-1.180.180", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40327-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40327-1.182.182", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GVLQDDADPMVSVMKMDKSP", "down_seq": "ESYSDIGGLESQIQEIKESV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr178" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40327-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40327-1.180.180", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40327-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40327-1.182.182", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQDDADPMVSVMKMDKSPTE", "down_seq": "YSDIGGLESQIQEIKESVEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser180" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40327-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40327-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40327-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40327-1.182.182", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QDDADPMVSVMKMDKSPTES", "down_seq": "SDIGGLESQIQEIKESVELP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Tyr181" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40327-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40327-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40327-1.180.180", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40327-1.182.182", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DDADPMVSVMKMDKSPTESY", "down_seq": "DIGGLESQIQEIKESVELPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser182" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40327-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40327-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40327-1.180.180", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40327-1.181.181", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LYGAPGTGKTLLAKAVANQT", "down_seq": "ATFLRIVGSELIQKYLGDGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser241" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40327-1.229.229", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40327-1.250.250", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLLAKAVANQTSATFLRIVG", "down_seq": "ELIQKYLGDGPRLCRQIFKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser250" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40327-1.241.241", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NAPSIVFIDEIDAIGTKRYD", "down_seq": "NSGGEREIQRTMLELLNQLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser294" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40327-1.296.296", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSIVFIDEIDAIGTKRYDSN", "down_seq": "GGEREIQRTMLELLNQLDGF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser296" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40327-1.294.294", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PALIRPGRIDRKILFENPDL", "down_seq": "TKKKILGIHTSKMNLSEDVN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser356" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40327-1.357.357", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40327-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "P40327-1", "length": 437, "uniprot_id": "PRS4_YEAST", "protein_name": "26S proteasome regulatory subunit 4 homolog", "refseq_ac": "NP_010277", "refseq_name": "proteasome regulatory particle base subunit RPT2", "gene_name": "RPT2", "gene_names_uniprotkb": "RPT2; D2920; YHS4; YTA5", "gene_names_refseq": "RPT2; YHS4; YTA5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40327", "url": "https://www.uniprot.org/uniprotkb/P40327" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ALIRPGRIDRKILFENPDLS", "down_seq": "KKKILGIHTSKMNLSEDVNL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002165", "url": "https://www.yeastgenome.org/locus/S000002165" }, { "database": "iPTMnet", "id": "P40327", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40327" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr357" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "229", "end_pos": "229" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40327-1.356.356", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40339-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P40339-1", "length": 323, "uniprot_id": "RFC4_YEAST", "protein_name": "Replication factor C subunit 4", "refseq_ac": "NP_014547", "refseq_name": "replication factor C subunit 4", "gene_name": "RFC4", "gene_names_uniprotkb": "RFC4; O0923", "gene_names_refseq": "RFC4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40339", "url": "https://www.uniprot.org/uniprotkb/P40339" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005454", "url": "https://www.yeastgenome.org/locus/S000005454", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSTRFAFACNQSNKIIEPLQ", "down_seq": "RCAILRYSKLSDEDVLKRLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005454", "url": "https://www.yeastgenome.org/locus/S000005454" }, { "database": "iPTMnet", "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser156" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "156", "end_pos": "156" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40339-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P40339-1", "length": 323, "uniprot_id": "RFC4_YEAST", "protein_name": "Replication factor C subunit 4", "refseq_ac": "NP_014547", "refseq_name": "replication factor C subunit 4", "gene_name": "RFC4", "gene_names_uniprotkb": "RFC4; O0923", "gene_names_refseq": "RFC4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40339", "url": "https://www.uniprot.org/uniprotkb/P40339" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005454", "url": "https://www.yeastgenome.org/locus/S000005454", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSKTL", "down_seq": "LQLPWVEKYRPQVLSDIVGN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005454", "url": "https://www.yeastgenome.org/locus/S000005454" }, { "database": "iPTMnet", "id": "P40339", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40339" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "156", "end_pos": "156" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40348-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P40348-1", "length": 353, "uniprot_id": "RFC2_YEAST", "protein_name": "Replication factor C subunit 2", "refseq_ac": "NP_012602", "refseq_name": "replication factor C subunit 2", "gene_name": "RFC2", "gene_names_uniprotkb": "RFC2; J1808", "gene_names_refseq": "RFC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40348", "url": "https://www.uniprot.org/uniprotkb/P40348" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40348", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40348" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003829", "url": "https://www.yeastgenome.org/locus/S000003829", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40348", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40348", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MFEGFGPNKKRKI", "down_seq": "KLAAEQSLAQQPWVEKYRPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003829", "url": "https://www.yeastgenome.org/locus/S000003829" }, { "database": "iPTMnet", "id": "P40348", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40348" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser14" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "277", "end_pos": "277" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40348-1.277.277", "start_pos": 277, "end_pos": 277, "uniprot_canonical_ac": "P40348-1", "length": 353, "uniprot_id": "RFC2_YEAST", "protein_name": "Replication factor C subunit 2", "refseq_ac": "NP_012602", "refseq_name": "replication factor C subunit 2", "gene_name": "RFC2", "gene_names_uniprotkb": "RFC2; J1808", "gene_names_refseq": "RFC2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40348", "url": "https://www.uniprot.org/uniprotkb/P40348" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40348", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40348" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003829", "url": "https://www.yeastgenome.org/locus/S000003829", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40348", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40348", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EELAGVVPHDILIEIVEKVK", "down_seq": "GDFDEIKKYVNTFMKSGWSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003829", "url": "https://www.yeastgenome.org/locus/S000003829" }, { "database": "iPTMnet", "id": "P40348", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40348" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser277" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "277", "end_pos": "277" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40352-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "P40352-1", "length": 1085, "uniprot_id": "RAD26_YEAST", "protein_name": "DNA repair and recombination protein RAD26", "refseq_ac": "NP_012569", "refseq_name": "DNA-dependent ATPase RAD26", "gene_name": "RAD26", "gene_names_uniprotkb": "RAD26; GTA1085; J1606", "gene_names_refseq": "RAD26", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEDKEQQDNAKLENNE", "down_seq": "LKDLGVNVLSQSSLEEKIAN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser17" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "870", "end_pos": "870" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P40352-1.27.27", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40352-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40352-1.30.30", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40352-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P40352-1", "length": 1085, "uniprot_id": "RAD26_YEAST", "protein_name": "DNA repair and recombination protein RAD26", "refseq_ac": "NP_012569", "refseq_name": "DNA-dependent ATPase RAD26", "gene_name": "RAD26", "gene_names_uniprotkb": "RAD26; GTA1085; J1606", "gene_names_refseq": "RAD26", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" }, { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "A role for checkpoint kinase-dependent Rad26 phosphorylation in transcription-coupled DNA repair in Saccharomyces cerevisiae.", "journal": "Molecular and cellular biology", "date": "2010-01", "authors": "Taschner Michael, Harreman Michelle, Teng Yumin, Gill Hefin, Anindya Roy, Maslen Sarah L, Skehel J Mark, Waters Raymond, Svejstrup Jesper Q", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "19901073", "url": "https://glygen.org/publication/PubMed/19901073" } ] }, { "title": "A proteome-wide analysis of kinase-substrate network in the DNA damage response.", "journal": "The Journal of biological chemistry", "date": "2010-04-23", "authors": "Chen Sheng-hong, Albuquerque Claudio P, Liang Jason, Suhandynata Raymond T, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19901073", "url": "https://glygen.org/publication/PubMed/19901073", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDNAKLENNESLKDLGVNVL", "down_seq": "QSSLEEKIANDVTNFSNLQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19901073", "url": "https://glygen.org/publication/PubMed/19901073" }, { "database": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" }, { "database": "SGD", "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser27" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "870", "end_pos": "870" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40352-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40352-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40352-1.30.30", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40352-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P40352-1", "length": 1085, "uniprot_id": "RAD26_YEAST", "protein_name": "DNA repair and recombination protein RAD26", "refseq_ac": "NP_012569", "refseq_name": "DNA-dependent ATPase RAD26", "gene_name": "RAD26", "gene_names_uniprotkb": "RAD26; GTA1085; J1606", "gene_names_refseq": "RAD26", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" }, { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NAKLENNESLKDLGVNVLSQ", "down_seq": "SLEEKIANDVTNFSNLQSLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser29" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "870", "end_pos": "870" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40352-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40352-1.27.27", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40352-1.30.30", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40352-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P40352-1", "length": 1085, "uniprot_id": "RAD26_YEAST", "protein_name": "DNA repair and recombination protein RAD26", "refseq_ac": "NP_012569", "refseq_name": "DNA-dependent ATPase RAD26", "gene_name": "RAD26", "gene_names_uniprotkb": "RAD26; GTA1085; J1606", "gene_names_refseq": "RAD26", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" }, { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKLENNESLKDLGVNVLSQS", "down_seq": "LEEKIANDVTNFSNLQSLQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" }, { "database": "SGD", "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser30" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "870", "end_pos": "870" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40352-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40352-1.27.27", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40352-1.29.29", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40352-1.863.863", "start_pos": 863, "end_pos": 863, "uniprot_canonical_ac": "P40352-1", "length": 1085, "uniprot_id": "RAD26_YEAST", "protein_name": "DNA repair and recombination protein RAD26", "refseq_ac": "NP_012569", "refseq_name": "DNA-dependent ATPase RAD26", "gene_name": "RAD26", "gene_names_uniprotkb": "RAD26; GTA1085; J1606", "gene_names_refseq": "RAD26", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ENLKNSKSEESDDFEQLVNL", "down_seq": "GVSKLESFYNGKEKKENSKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796" }, { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser863" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "870", "end_pos": "870" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P40352-1.870.870", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40352-1.870.870", "start_pos": 870, "end_pos": 870, "uniprot_canonical_ac": "P40352-1", "length": 1085, "uniprot_id": "RAD26_YEAST", "protein_name": "DNA repair and recombination protein RAD26", "refseq_ac": "NP_012569", "refseq_name": "DNA-dependent ATPase RAD26", "gene_name": "RAD26", "gene_names_uniprotkb": "RAD26; GTA1085; J1606", "gene_names_refseq": "RAD26", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40352", "url": "https://www.uniprot.org/uniprotkb/P40352" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEESDDFEQLVNLSGVSKLE", "down_seq": "FYNGKEKKENSKTEDDRLIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003796", "url": "https://www.yeastgenome.org/locus/S000003796" }, { "database": "iPTMnet", "id": "P40352", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40352" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser870" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "17", "end_pos": "17" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "870", "end_pos": "870" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40352-1.863.863", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NHSNSTLNVGPSRQTRQPPV", "down_seq": "TSTNSLSLDQRSPLANPMQE", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser208", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" } ], "site_lbl": "Ser208" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40357-1.215.215", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HSNSTLNVGPSRQTRQPPVS", "down_seq": "STNSLSLDQRSPLANPMQEK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr209", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr209" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40357-1.215.215", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNSTLNVGPSRQTRQPPVST", "down_seq": "TNSLSLDQRSPLANPMQEKR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser210", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser210" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40357-1.215.215", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLNVGPSRQTRQPPVSTSTN", "down_seq": "LSLDQRSPLANPMQEKRNPY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser213", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser213" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.215.215", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NVGPSRQTRQPPVSTSTNSL", "down_seq": "LDQRSPLANPMQEKRNPYAD", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser215", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTNRSSGTRQGSSKNANPYA", "down_seq": "MANDSYSNGNLNRSANPYSS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser266", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40357-1.271.271", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40357-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40357-1.273.273", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGTRQGSSKNANPYASMAND", "down_seq": "YSNGNLNRSANPYSSRSVRQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser271", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser271" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40357-1.266.266", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40357-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.273.273", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRQGSSKNANPYASMANDSY", "down_seq": "NGNLNRSANPYSSRSVRQPQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser273", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser273" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40357-1.266.266", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.271.271", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40357-1.272.272", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ADEKVAELKKLNRSILAVHV", "down_seq": "NPFNSKRRRREREEQLKNRK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser509", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40357-1.514.514", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.514.514", "start_pos": 514, "end_pos": 514, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AELKKLNRSILAVHVSNPFN", "down_seq": "KRRRREREEQLKNRKIEEKL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser514", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40357-1.509.509", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.540.540", "start_pos": 540, "end_pos": 540, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EREEQLKNRKIEEKLMREQT", "down_seq": "QQLSQSTQRIEGAMNANNNI", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser540", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser540" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40357-1.539.539", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40357-1.544.544", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40357-1.546.546", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.544.544", "start_pos": 544, "end_pos": 544, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLKNRKIEEKLMREQTSQQL", "down_seq": "QSTQRIEGAMNANNNISEVR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser544", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40357-1.539.539", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40357-1.540.540", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.546.546", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.546.546", "start_pos": 546, "end_pos": 546, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KNRKIEEKLMREQTSQQLSQ", "down_seq": "TQRIEGAMNANNNISEVRER", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser546", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40357" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser546" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40357-1.539.539", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40357-1.540.540", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.544.544", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" }, { "database": "O-GlcNAc Atlas", "id": "P40357", "url": "https://oglcnac.org/atlas/detail/P40357" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40357", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YNGTSLNSYNNDGPYSNQNT", "down_seq": "NSWVNANGRNSLNHSNSTLN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser175" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40357-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40357-1.186.186", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GTSLNSYNNDGPYSNQNTSN", "down_seq": "WVNANGRNSLNHSNSTLNVG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser177" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40357-1.175.175", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40357-1.186.186", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DGPYSNQNTSNSWVNANGRN", "down_seq": "LNHSNSTLNVGPSRQTRQPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser186" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40357-1.175.175", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40357-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNQNTSNSWVNANGRNSLNH", "down_seq": "NSTLNVGPSRQTRQPPVSTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser190" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40357-1.175.175", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40357-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40357-1.186.186", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNTSNSWVNANGRNSLNHSN", "down_seq": "TLNVGPSRQTRQPPVSTSTN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser192" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40357-1.175.175", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40357-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40357-1.186.186", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NTSNSWVNANGRNSLNHSNS", "down_seq": "LNVGPSRQTRQPPVSTSTNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr193" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40357-1.175.175", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40357-1.177.177", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40357-1.186.186", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40357-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSTLNVGPSRQTRQPPVSTS", "down_seq": "NSLSLDQRSPLANPMQEKRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr211" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40357-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P40357-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40357-1.215.215", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQTRQPPVSTSTNSLSLDQR", "down_seq": "PLANPMQEKRNPYADMNSYG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser220" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40357-1.208.208", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40357-1.209.209", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40357-1.210.210", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40357-1.211.211", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40357-1.213.213", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40357-1.215.215", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40357-1.238.238", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRSPLANPMQEKRNPYADMN", "down_seq": "YGGAYDSNTNRSSGTRQGSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser238" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40357-1.220.220", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GTRQGSSKNANPYASMANDS", "down_seq": "SNGNLNRSANPYSSRSVRQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Tyr272" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40357-1.266.266", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40357-1.271.271", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40357-1.273.273", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YSSRSVRQPQSQQAPMTYTP", "down_seq": "FIASDEAARNSEVDLNEEPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser304" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40357-1.308.308", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40357-1.315.315", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVRQPQSQQAPMTYTPSFIA", "down_seq": "DEAARNSEVDLNEEPRTGEF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser308" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40357-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40357-1.315.315", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQAPMTYTPSFIASDEAARN", "down_seq": "EVDLNEEPRTGEFDFEEVYA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser315" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40357-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40357-1.308.308", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLNEEPRTGEFDFEEVYADK", "down_seq": "AENRAALDEPDLNAVMTNED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser338" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P40357-1.355.355", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ADKSAENRAALDEPDLNAVM", "down_seq": "NEDSIDLNASEVDHSSRQQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" } ], "site_lbl": "Thr355" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40357-1.338.338", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40357-1.359.359", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AENRAALDEPDLNAVMTNED", "down_seq": "IDLNASEVDHSSRQQQQQQW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser359" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40357-1.355.355", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQEEDEAVDEIKQEIKFTKQ", "down_seq": "SVASTRNTLKMAQDAERAGM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser439" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40357-1.443.443", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.443.443", "start_pos": 443, "end_pos": 443, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEAVDEIKQEIKFTKQSSVA", "down_seq": "TRNTLKMAQDAERAGMNTLG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser443" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40357-1.439.439", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.539.539", "start_pos": 539, "end_pos": 539, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "REREEQLKNRKIEEKLMREQ", "down_seq": "SQQLSQSTQRIEGAMNANNN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr539" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40357-1.540.540", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40357-1.544.544", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40357-1.546.546", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALTTGKELDSQQKRLNNIEE", "down_seq": "TDDLDINLHMNTNRLAGIR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser632" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APPGYEQYARPQDELEDLNA", "down_seq": "PLDANANEATAGSNRGSSGT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser79" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P40357-1.89.89", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40357-1.92.92", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PQDELEDLNASPLDANANEA", "down_seq": "AGSNRGSSGTQDLGNGAESN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr89" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40357-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40357-1.92.92", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40357-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P40357-1", "length": 651, "uniprot_id": "SEC9_YEAST", "protein_name": "Protein transport protein SEC9", "refseq_ac": "NP_011523", "refseq_name": "Sec9p", "gene_name": "SEC9", "gene_names_uniprotkb": "SEC9; HSS7", "gene_names_refseq": "HSS7; SEC9", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELEDLNASPLDANANEATAG", "down_seq": "NRGSSGTQDLGNGAESNSMQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40357", "url": "https://www.uniprot.org/uniprotkb/P40357" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40357", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40357" }, { "database": "SGD", "id": "S000003241", "url": "https://www.yeastgenome.org/locus/S000003241" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser92" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "514", "end_pos": "514" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "544", "end_pos": "544" }, { "start_pos": "546", "end_pos": "546" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "175", "end_pos": "175" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "359", "end_pos": "359" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "539", "end_pos": "539" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40357-1.79.79", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40357-1.89.89", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40452-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P40452-1", "length": 197, "uniprot_id": "COA1_YEAST", "protein_name": "Cytochrome c oxidase assembly factor 1", "refseq_ac": "NP_012109", "refseq_name": "Coa1p", "gene_name": "COA1", "gene_names_uniprotkb": "COA1; FMP35", "gene_names_refseq": "COA1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40452", "url": "https://www.uniprot.org/uniprotkb/P40452" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40452", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40452" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] } ], "crossref": [ { "id": "P40452", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40452", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LNSVKGRINITFYIKGDKNV", "down_seq": "GTVRLVADRNTHDEEFLIHE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40452", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40452" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ], "site_lbl": "Thr156" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "156", "end_pos": "156" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "APNLEPNDQLKLALLPEVIP", "down_seq": "PAFREPERKTSVPVRPSVLL", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr218", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P40453-1.229.229", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40453-1.235.235", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40453-1.844.844", "start_pos": 844, "end_pos": 844, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FTSDEVLSGENAWDCPRCGP", "down_seq": "ASVSTSVSALENEPSIVKSK", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr844", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P40453-1.852.852", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40453-1.863.863", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40453-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SLQFQTRNKSYSIYTDLKKM", "down_seq": "ENEMNMTNVVLMVKKEIGVV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Tyr113" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P40453-1.120.120", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NKSYSIYTDLKKMYENEMNM", "down_seq": "NVVLMVKKEIGVVLDESVKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Thr120" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40453-1.113.113", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DESVKHGAGIEHRITKKRAF", "down_seq": "VPADDLSGQVASLSLDTAAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser155" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GQVASLSLDTAAPQDHGLKG", "down_seq": "FTEDDAEQSSPVWTAPNLEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr183" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P40453-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40453-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40453-1.197.197", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAAPQDHGLKGTFTEDDAEQ", "down_seq": "SPVWTAPNLEPNDQLKLALL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser192" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40453-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40453-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40453-1.197.197", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAPQDHGLKGTFTEDDAEQS", "down_seq": "PVWTAPNLEPNDQLKLALLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser193" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40453-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40453-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40453-1.197.197", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DHGLKGTFTEDDAEQSSPVW", "down_seq": "APNLEPNDQLKLALLPEVIP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr197" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40453-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40453-1.192.192", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40453-1.193.193", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LALLPEVIPTPAFREPERKT", "down_seq": "VPVRPSVLLEDVPSIYHEDD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser229" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40453-1.218.218", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40453-1.235.235", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VIPTPAFREPERKTSVPVRP", "down_seq": "VLLEDVPSIYHEDDTSFASL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser235" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40453-1.218.218", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40453-1.229.229", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.486.486", "start_pos": 486, "end_pos": 486, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKARLQQEQQQQQQQPDSQD", "down_seq": "FSAKESSTKVPEPPSWKPPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser486" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40453-1.488.488", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.488.488", "start_pos": 488, "end_pos": 488, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARLQQEQQQQQQQPDSQDSF", "down_seq": "AKESSTKVPEPPSWKPPDLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser488" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40453-1.486.486", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.810.810", "start_pos": 810, "end_pos": 810, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FYVLSLAIPRRSMKLSKLGR", "down_seq": "TEKRVKLEDCINMFTSDEVL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser810" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.852.852", "start_pos": 852, "end_pos": 852, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GENAWDCPRCGPTASVSTSV", "down_seq": "ALENEPSIVKSKKKKSRFFT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser852" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40453-1.844.844", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40453-1.863.863", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40453-1.868.868", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.863.863", "start_pos": 863, "end_pos": 863, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PTASVSTSVSALENEPSIVK", "down_seq": "KKKKSRFFTLHTGTKRRHLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser863" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40453-1.844.844", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40453-1.852.852", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40453-1.868.868", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.868.868", "start_pos": 868, "end_pos": 868, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cell cycle phosphorylation of mitotic exit network (MEN) proteins.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2011-10-15", "authors": "Jones Michele H, Keck Jamie M, Wong Catherine C L, Xu Tao, Yates John R, Winey Mark", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSVSALENEPSIVKSKKKK", "down_seq": "RFFTLHTGTKRRHLDFFGDG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "22031224", "url": "https://glygen.org/publication/PubMed/22031224" } ], "site_lbl": "Ser868" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40453-1.852.852", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40453-1.863.863", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.910.910", "start_pos": 910, "end_pos": 910, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TEGHNSNNNNTTIFERERSR", "down_seq": "PFRMLGGSGKRSSSSTPFST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser910" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P40453-1.918.918", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40453-1.924.924", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40453-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40453-1.926.926", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.918.918", "start_pos": 918, "end_pos": 918, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNTTIFERERSRSPFRMLGG", "down_seq": "GKRSSSSTPFSTGGNDSNNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser918" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40453-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40453-1.924.924", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40453-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40453-1.926.926", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.924.924", "start_pos": 924, "end_pos": 924, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERERSRSPFRMLGGSGKRSS", "down_seq": "STPFSTGGNDSNNSSDYKNK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser924" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40453-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40453-1.918.918", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40453-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40453-1.926.926", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.925.925", "start_pos": 925, "end_pos": 925, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RERSRSPFRMLGGSGKRSSS", "down_seq": "TPFSTGGNDSNNSSDYKNKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser925" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40453-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40453-1.918.918", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40453-1.924.924", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40453-1.926.926", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40453-1.926.926", "start_pos": 926, "end_pos": 926, "uniprot_canonical_ac": "P40453-1", "length": 1071, "uniprot_id": "UBP7_YEAST", "protein_name": "Ubiquitin carboxyl-terminal hydrolase 7", "refseq_ac": "NP_012110", "refseq_name": "ubiquitin-specific protease UBP7", "gene_name": "UBP7", "gene_names_uniprotkb": "UBP7", "gene_names_refseq": "UBP7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40453", "url": "https://www.uniprot.org/uniprotkb/P40453" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ERSRSPFRMLGGSGKRSSSS", "down_seq": "PFSTGGNDSNNSSDYKNKKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001418", "url": "https://www.yeastgenome.org/locus/S000001418" }, { "database": "iPTMnet", "id": "P40453", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40453" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr926" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "218", "end_pos": "218" }, { "start_pos": "844", "end_pos": "844" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "852", "end_pos": "852" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "868", "end_pos": "868" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "924", "end_pos": "924" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "926", "end_pos": "926" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40453-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40453-1.918.918", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40453-1.924.924", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40453-1.925.925", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.359.359", "start_pos": 359, "end_pos": 359, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IVMDCTKEEEATMTTSAVSP", "down_seq": "VGKLFSDIKVLKRQLIKERN", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr359", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40457-1.357.357", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40457-1.761.761", "start_pos": 761, "end_pos": 761, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40457", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40457" }, { "database": "O-GlcNAc Atlas", "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FEQCCKEKKELQMRLKESEI", "down_seq": "HNENKMDFSSKEGQYKAKIK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser761", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40457", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40457" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P40457-1.770.770", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40457-1.771.771", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.770.770", "start_pos": 770, "end_pos": 770, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40457", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40457" }, { "database": "O-GlcNAc Atlas", "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELQMRLKESEISHNENKMDF", "down_seq": "SKEGQYKAKIKELENNLERL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser770", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40457", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40457" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40457-1.761.761", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40457-1.771.771", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.771.771", "start_pos": 771, "end_pos": 771, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40457", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40457" }, { "database": "O-GlcNAc Atlas", "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQMRLKESEISHNENKMDFS", "down_seq": "KEGQYKAKIKELENNLERLR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser771", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40457", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40457" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40457-1.761.761", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40457-1.770.770", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40457", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40457" }, { "database": "O-GlcNAc Atlas", "id": "P40457", "url": "https://oglcnac.org/atlas/detail/P40457" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40457", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40457", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40457", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40457" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P40457-1.6.6", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1007.1007", "start_pos": 1007, "end_pos": 1007, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EKMSTIVQLCKKKEMSQYQS", "down_seq": "MKENKDLSELVIRLEKDAAD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr1007" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P40457-1.1015.1015", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1015.1015", "start_pos": 1015, "end_pos": 1015, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] } ], "crossref": [ { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LCKKKEMSQYQSTMKENKDL", "down_seq": "ELVIRLEKDAADCQAELTKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" } ], "site_lbl": "Ser1015" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40457-1.1007.1007", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40457-1.1035.1035", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1035.1035", "start_pos": 1035, "end_pos": 1035, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SELVIRLEKDAADCQAELTK", "down_seq": "KSSLYSAQDLLDKHERKWME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Thr1035" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40457-1.1015.1015", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40457-1.1037.1037", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40457-1.1038.1038", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1037.1037", "start_pos": 1037, "end_pos": 1037, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LVIRLEKDAADCQAELTKTK", "down_seq": "SLYSAQDLLDKHERKWMEEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1037" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40457-1.1035.1035", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40457-1.1038.1038", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1038.1038", "start_pos": 1038, "end_pos": 1038, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VIRLEKDAADCQAELTKTKS", "down_seq": "LYSAQDLLDKHERKWMEEKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1038" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40457-1.1035.1035", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40457-1.1037.1037", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1079.1079", "start_pos": 1079, "end_pos": 1079, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DYERELISNIEQTESLRVEN", "down_seq": "VLIEKVDDTAANNGDKDHLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1079" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1105.1105", "start_pos": 1105, "end_pos": 1105, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VDDTAANNGDKDHLKLVSLF", "down_seq": "NLRHERNSLETKLTTCKREL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1105" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1346.1346", "start_pos": 1346, "end_pos": 1346, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HFENAKVIDLDTKLKAHELQ", "down_seq": "EDVSRDHEKDTYRTLMEEIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1346" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40457-1.1350.1350", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1350.1350", "start_pos": 1350, "end_pos": 1350, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKVIDLDTKLKAHELQSEDV", "down_seq": "RDHEKDTYRTLMEEIESLKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1350" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40457-1.1346.1346", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEKRVKEEYDIWQSRDQGND", "down_seq": "LNDDLNKENKLLRRKLMEME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser137" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1381.1381", "start_pos": 1381, "end_pos": 1381, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMEEIESLKKELQIFKTANS", "down_seq": "SDAFEKLKVNMEKEKDRIID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1381" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1420.1420", "start_pos": 1420, "end_pos": 1420, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IDERTKEFEKKLQETLNKST", "down_seq": "SEAEYSKDIETLKKEWLKEY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1420" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40457-1.1421.1421", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1421.1421", "start_pos": 1421, "end_pos": 1421, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DERTKEFEKKLQETLNKSTS", "down_seq": "EAEYSKDIETLKKEWLKEYE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1421" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40457-1.1420.1420", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1463.1463", "start_pos": 1463, "end_pos": 1463, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETLRRIKEAEENLKKRIRLP", "down_seq": "EERIQKIISKRKEELEEEFR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1463" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1492.1492", "start_pos": 1492, "end_pos": 1492, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKRKEELEEEFRKKLKENAG", "down_seq": "LTFLDNKGSGEDAEEELWNS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1492" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P40457-1.1501.1501", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40457-1.1512.1512", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1501.1501", "start_pos": 1501, "end_pos": 1501, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EFRKKLKENAGSLTFLDNKG", "down_seq": "GEDAEEELWNSPSKGNSERP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1501" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40457-1.1492.1492", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40457-1.1512.1512", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40457-1.1514.1514", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40457-1.1518.1518", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1512.1512", "start_pos": 1512, "end_pos": 1512, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLTFLDNKGSGEDAEEELWN", "down_seq": "PSKGNSERPSAVAGFINQKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1512" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40457-1.1492.1492", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40457-1.1501.1501", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40457-1.1514.1514", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40457-1.1518.1518", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1514.1514", "start_pos": 1514, "end_pos": 1514, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TFLDNKGSGEDAEEELWNSP", "down_seq": "KGNSERPSAVAGFINQKNLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1514" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40457-1.1501.1501", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40457-1.1512.1512", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40457-1.1518.1518", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1518.1518", "start_pos": 1518, "end_pos": 1518, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NKGSGEDAEEELWNSPSKGN", "down_seq": "ERPSAVAGFINQKNLKPQEQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1518" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40457-1.1501.1501", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40457-1.1512.1512", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40457-1.1514.1514", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1547.1547", "start_pos": 1547, "end_pos": 1547, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FINQKNLKPQEQLKNVKNDV", "down_seq": "FNDSQSMVTNKENNIVDSSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1547" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1577.1577", "start_pos": 1577, "end_pos": 1577, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NKENNIVDSSAAGNKAIPTF", "down_seq": "FGKPFFSSNTSSLQSFQNPF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1577" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1656.1656", "start_pos": 1656, "end_pos": 1656, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSTDGAKITEIGSTSKRPIE", "down_seq": "GTSSDPDTKKVKESPANDQA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1656" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P40457-1.1659.1659", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40457-1.1660.1660", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40457-1.1670.1670", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1659.1659", "start_pos": 1659, "end_pos": 1659, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DGAKITEIGSTSKRPIESGT", "down_seq": "SDPDTKKVKESPANDQASNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1659" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40457-1.1656.1656", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40457-1.1660.1660", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40457-1.1670.1670", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40457-1.1677.1677", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1660.1660", "start_pos": 1660, "end_pos": 1660, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAKITEIGSTSKRPIESGTS", "down_seq": "DPDTKKVKESPANDQASNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1660" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40457-1.1656.1656", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40457-1.1659.1659", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40457-1.1670.1670", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40457-1.1677.1677", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1670.1670", "start_pos": 1670, "end_pos": 1670, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKRPIESGTSSDPDTKKVKE", "down_seq": "PANDQASNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1670" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40457-1.1656.1656", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40457-1.1659.1659", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40457-1.1660.1660", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40457-1.1677.1677", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.1677.1677", "start_pos": 1677, "end_pos": 1677, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GTSSDPDTKKVKESPANDQA", "down_seq": "NE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1677" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40457-1.1659.1659", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P40457-1.1660.1660", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40457-1.1670.1670", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVQEKELMLQSKKLIEEKLS", "down_seq": "FSKKTLTEEVTKSSHVENLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser197" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLSQSVEEKVLEMKNLKDTA", "down_seq": "VEKAEFSKEMTLQKNMNDLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser263" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQKNMNDLLRSQLTSLEKDC", "down_seq": "LRAIEKNDDNSCRNPEHTDV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser295" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNIVMDCTKEEEATMTTSAV", "down_seq": "PTVGKLFSDIKVLKRQLIKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser357" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40457-1.359.359", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FILELEHKTPELISFKERTK", "down_seq": "LEHELKRSTELLETVSLTKR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser411" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.595.595", "start_pos": 595, "end_pos": 595, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KMETRINILLRERDSYKLLA", "down_seq": "TEENKANTNSVTSMEAAREK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser595" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P40457-1.608.608", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.608.608", "start_pos": 608, "end_pos": 608, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSYKLLASTEENKANTNSVT", "down_seq": "MEAAREKKIRELEAELSSTK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser608" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40457-1.595.595", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEDKI", "down_seq": "EFLNVPFESLQGVTYPVLRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40457-1.0.0", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science", "date": "2009", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YYSRISKLKQLLDESSEQKN", "down_seq": "AKEELNGLKDQLNEERSRYR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" } ], "site_lbl": "Thr75" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40457-1.845.845", "start_pos": 845, "end_pos": 845, "uniprot_canonical_ac": "P40457-1", "length": 1679, "uniprot_id": "MLP2_YEAST", "protein_name": "Protein MLP2", "refseq_ac": "NP_012117", "refseq_name": "Mlp2p", "gene_name": "MLP2", "gene_names_uniprotkb": "MLP2", "gene_names_refseq": "MLP2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40457", "url": "https://www.uniprot.org/uniprotkb/P40457" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KMKSLLTELSNKETTIEKLS", "down_seq": "EIENLDKELRKTKFQYKFLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001411", "url": "https://www.yeastgenome.org/locus/S000001411" }, { "database": "iPTMnet", "id": "P40457", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40457" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser845" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "359", "end_pos": "359" }, { "start_pos": "761", "end_pos": "761" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "771", "end_pos": "771" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1038", "end_pos": "1038" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1105", "end_pos": "1105" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "1350", "end_pos": "1350" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1381", "end_pos": "1381" }, { "start_pos": "1420", "end_pos": "1420" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1501", "end_pos": "1501" }, { "start_pos": "1512", "end_pos": "1512" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "1518", "end_pos": "1518" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1577", "end_pos": "1577" }, { "start_pos": "1656", "end_pos": "1656" }, { "start_pos": "1659", "end_pos": "1659" }, { "start_pos": "1660", "end_pos": "1660" }, { "start_pos": "1670", "end_pos": "1670" }, { "start_pos": "1677", "end_pos": "1677" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "845", "end_pos": "845" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphorylation of the mitotic regulator protein Hec1 by Nek2 kinase is essential for faithful chromosome segregation.", "journal": "The Journal of biological chemistry", "date": "2002", "authors": "Chen Y, Riley DJ, Zheng L, Chen PL, Lee WH", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "reference": [ { "type": "PubMed", "id": "12386167", "url": "https://glygen.org/publication/PubMed/12386167" } ] } ], "crossref": [ { "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12386167", "url": "https://glygen.org/publication/PubMed/12386167", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSIENEIYQILKNLRYPFLE", "down_seq": "INKSQISAVGGSNWHKFLGM", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Loss of function.", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" }, { "database": "PubMed", "id": "12386167", "url": "https://glygen.org/publication/PubMed/12386167" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40460-1.205.205", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40460-1.208.208", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40460-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phospho-regulation of kinetochore-microtubule attachments by the Aurora kinase Ipl1p.", "journal": "Cell", "date": "2002", "authors": "Cheeseman IM, Anderson S, Jwa M, Green EM, Kang Js, Yates JR 3rd, Chan CS, Drubin DG, Barnes G", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "12408861", "url": "https://glygen.org/publication/PubMed/12408861" } ] }, { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12408861", "url": "https://glygen.org/publication/PubMed/12408861", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NGTALALNDKSNSRNSVSRL", "down_seq": "INQLGSLQQHLSNRDPRPLR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "12408861", "url": "https://glygen.org/publication/PubMed/12408861" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser100" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NEIYQILKNLRYPFLESINK", "down_seq": "QISAVGGSNWHKFLGMLHWM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ], "site_lbl": "Ser205" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40460-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40460-1.208.208", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40460-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YQILKNLRYPFLESINKSQI", "down_seq": "AVGGSNWHKFLGMLHWMVRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser208" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40460-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40460-1.205.205", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40460-1.213.213", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NLRYPFLESINKSQISAVGG", "down_seq": "NWHKFLGMLHWMVRTNIKLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser213" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40460-1.201.201", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40460-1.205.205", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40460-1.208.208", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MQSSTSTDQHVLHHMDPHRF", "down_seq": "SQIPTATSSQLRRRNSTNQG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ], "site_lbl": "Thr21" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40460-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40460-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40460-1.6.6", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40460-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40460-1.37.37", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40460-1.38.38", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSSTSTDQHVLHHMDPHRFT", "down_seq": "QIPTATSSQLRRRNSTNQGL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ], "site_lbl": "Ser22" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40460-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P40460-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40460-1.6.6", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40460-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40460-1.37.37", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40460-1.38.38", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Aurora B-dependent Ndc80 degradation regulates kinetochore composition in meiosis.", "journal": "Genes & development", "date": "2020-02-01", "authors": "Chen Jingxun, Liao Andrew, Powers Emily N, Liao Hanna, Kohlstaedt Lori A, Evans Rena, Holly Ryan M, Kim Jenny Kim, Jovanovic Marko, \u00dcnal El\u00e7in", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "31919192", "url": "https://glygen.org/publication/PubMed/31919192" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31919192", "url": "https://glygen.org/publication/PubMed/31919192", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TNIKLDMCLNKVDRSLINQN", "down_seq": "QEITILSQPLKTLDEQDQRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "31919192", "url": "https://glygen.org/publication/PubMed/31919192" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr248" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40460-1.252.252", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDMCLNKVDRSLINQNTQEI", "down_seq": "ILSQPLKTLDEQDQRQERYE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr252" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40460-1.248.248", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.345.345", "start_pos": 345, "end_pos": 345, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QNDNLYEKYQEVMKISQKIK", "down_seq": "TREKWKALKSDSNKYENYVN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Thr345" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae.", "journal": "Genetics", "date": "2009-12", "authors": "Akiyoshi Bungo, Nelson Christian R, Ranish Jeffrey A, Biggins Sue", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PHRFTSQIPTATSSQLRRRN", "down_seq": "TNQGLTDMINKSIARNTISG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser37" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40460-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40460-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40460-1.38.38", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40460-1.43.43", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40460-1.54.54", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.383.383", "start_pos": 383, "end_pos": 383, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YVNAMKQKSQEWPGKLEKMK", "down_seq": "ECELKEEEIKALQSNISELH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser383" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HRFTSQIPTATSSQLRRRNS", "down_seq": "NQGLTDMINKSIARNTISGT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr38" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40460-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40460-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40460-1.37.37", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40460-1.43.43", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40460-1.54.54", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QIPTATSSQLRRRNSTNQGL", "down_seq": "DMINKSIARNTISGTGIPTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr43" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40460-1.37.37", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40460-1.38.38", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40460-1.54.54", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.477.477", "start_pos": 477, "end_pos": 477, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLLDTLRQYDSSIQNLTRSR", "down_seq": "QLGHNVNDSSLKINISENLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser477" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P40460-1.486.486", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40460-1.487.487", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.486.486", "start_pos": 486, "end_pos": 486, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSSIQNLTRSRSQLGHNVND", "down_seq": "SLKINISENLLDRDFHEGIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser486" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P40460-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40460-1.487.487", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.487.487", "start_pos": 487, "end_pos": 487, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSIQNLTRSRSQLGHNVNDS", "down_seq": "LKINISENLLDRDFHEGISY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser487" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40460-1.477.477", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40460-1.486.486", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MQS", "down_seq": "TSTDQHVLHHMDPHRFTSQI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ], "site_lbl": "Ser4" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P40460-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40460-1.6.6", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40460-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40460-1.22.22", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae.", "journal": "Genetics", "date": "2009-12", "authors": "Akiyoshi Bungo, Nelson Christian R, Ranish Jeffrey A, Biggins Sue", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Aurora B-dependent Ndc80 degradation regulates kinetochore composition in meiosis.", "journal": "Genes & development", "date": "2020-02-01", "authors": "Chen Jingxun, Liao Andrew, Powers Emily N, Liao Hanna, Kohlstaedt Lori A, Evans Rena, Holly Ryan M, Kim Jenny Kim, Jovanovic Marko, \u00dcnal El\u00e7in", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "31919192", "url": "https://glygen.org/publication/PubMed/31919192" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31919192", "url": "https://glygen.org/publication/PubMed/31919192", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RRNSTNQGLTDMINKSIARN", "down_seq": "ISGTGIPTGGINKNKRTRST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "31919192", "url": "https://glygen.org/publication/PubMed/31919192" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr54" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40460-1.37.37", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P40460-1.38.38", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40460-1.43.43", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40460-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40460-1.74.74", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MQSS", "down_seq": "STDQHVLHHMDPHRFTSQIP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ], "site_lbl": "Thr5" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P40460-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40460-1.6.6", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40460-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40460-1.22.22", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.612.612", "start_pos": 612, "end_pos": 612, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QRIEIEKMEKKINDSNLLMK", "down_seq": "KISDAEELVTSTELKLEELK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" } ], "site_lbl": "Thr612" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.685.685", "start_pos": 685, "end_pos": 685, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ENSENELGNVIEELRNLEFE", "down_seq": "EHNVTN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr685" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40460-1.690.690", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.690.690", "start_pos": 690, "end_pos": 690, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ELGNVIEELRNLEFETEHNV", "down_seq": "", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr690" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40460-1.685.685", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mimicking Ndc80 phosphorylation triggers spindle assembly checkpoint signalling.", "journal": "The EMBO journal", "date": "2009-04-22", "authors": "Kemmler Stefan, Stach Manuel, Knapp Maria, Ortiz Jennifer, Pfannstiel Jens, Ruppert Thomas, Lechner Johannes", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ] } ], "crossref": [ { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MQSST", "down_seq": "TDQHVLHHMDPHRFTSQIPT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19300438", "url": "https://glygen.org/publication/PubMed/19300438" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40460-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40460-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40460-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40460-1.22.22", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ARNTISGTGIPTGGINKNKR", "down_seq": "RSTVAGGTNGTALALNDKSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr71" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40460-1.54.54", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40460-1.74.74", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40460-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae.", "journal": "Genetics", "date": "2009-12", "authors": "Akiyoshi Bungo, Nelson Christian R, Ranish Jeffrey A, Biggins Sue", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TISGTGIPTGGINKNKRTRS", "down_seq": "VAGGTNGTALALNDKSNSRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "19822728", "url": "https://glygen.org/publication/PubMed/19822728" } ], "site_lbl": "Thr74" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40460-1.54.54", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40460-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40460-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40460-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P40460-1", "length": 691, "uniprot_id": "NDC80_YEAST", "protein_name": "Kinetochore protein NDC80", "refseq_ac": "NP_012122", "refseq_name": "kinetochore-associated Ndc80 complex subunit NDC80", "gene_name": "NDC80", "gene_names_uniprotkb": "NDC80; HEC1; TID3", "gene_names_refseq": "HEC1; NDC80; TID3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40460", "url": "https://www.uniprot.org/uniprotkb/P40460" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GIPTGGINKNKRTRSTVAGG", "down_seq": "NGTALALNDKSNSRNSVSRL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001406", "url": "https://www.yeastgenome.org/locus/S000001406" }, { "database": "iPTMnet", "id": "P40460", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40460" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr79" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "201", "end_pos": "201" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40460-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40460-1.74.74", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGNHEDDNDDDSSGDEKDID", "down_seq": "EDEQDPFESHFNQVPEKFVD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser155" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VDKLSNAFKTKSVKYKSVKG", "down_seq": "LSDSESYIYAKPVVIGEEAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser194" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40498-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40498-1.200.200", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLSNAFKTKSVKYKSVKGSL", "down_seq": "DSESYIYAKPVVIGEEALVE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser196" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40498-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40498-1.200.200", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AFKTKSVKYKSVKGSLSDSE", "down_seq": "YIYAKPVVIGEEALVESPYR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser200" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40498-1.194.194", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40498-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40498-1.217.217", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSESYIYAKPVVIGEEALVE", "down_seq": "PYRSSSIYSYFLKQRLKVQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser217" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40498-1.200.200", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "DSSVREKNDNFRGYRKRGRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRGRQELRKIKRSSARTEGG", "down_seq": "TETLEDVAEDIDHRSDEDEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser38" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P40498-1.53.53", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DFFVVGLKFTRKAIKLYSNF", "down_seq": "QSDIIVCSPLGIQMILENTD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Tyr402" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40498-1.404.404", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FVVGLKFTRKAIKLYSNFYQ", "down_seq": "DIIVCSPLGIQMILENTDKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser404" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40498-1.402.402", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RTEGGSTETLEDVAEDIDHR", "down_seq": "DEDEVSDVDSGDDFDIEDEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" } ], "site_lbl": "Ser53" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40498-1.38.38", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40498-1.59.59", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40498-1.63.63", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TETLEDVAEDIDHRSDEDEV", "down_seq": "DVDSGDDFDIEDEEGKKEKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" } ], "site_lbl": "Ser59" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40498-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40498-1.63.63", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40498-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P40498-1", "length": 721, "uniprot_id": "UTP25_YEAST", "protein_name": "U3 small nucleolar RNA-associated protein 25", "refseq_ac": "NP_012175", "refseq_name": "rRNA-binding ribosome biosynthesis protein UTP25", "gene_name": "UTP25", "gene_names_uniprotkb": "UTP25", "gene_names_refseq": "UTP25", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EDVAEDIDHRSDEDEVSDVD", "down_seq": "GDDFDIEDEEGKKEKVYDAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40498", "url": "https://www.uniprot.org/uniprotkb/P40498" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40498", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40498" }, { "database": "SGD", "id": "S000001353", "url": "https://www.yeastgenome.org/locus/S000001353" } ], "site_lbl": "Ser63" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "155", "end_pos": "155" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "63", "end_pos": "63" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40498-1.53.53", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40498-1.59.59", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40506-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P40506-1", "length": 365, "uniprot_id": "PPCS_YEAST", "protein_name": "Phosphopantothenate--cysteine ligase CAB2", "refseq_ac": "NP_012183", "refseq_name": "phosphopantothenate--cysteine ligase CAB2", "gene_name": "CAB2", "gene_names_uniprotkb": "CAB2", "gene_names_refseq": "CAB2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40506", "url": "https://www.uniprot.org/uniprotkb/P40506" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001345", "url": "https://www.yeastgenome.org/locus/S000001345", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GTTVPLENNTVRFIDNFSAG", "down_seq": "RGASSAEQFLANGYSVIFLH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001345", "url": "https://www.yeastgenome.org/locus/S000001345" }, { "database": "iPTMnet", "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr102" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40506-1.99.99", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40506-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P40506-1", "length": 365, "uniprot_id": "PPCS_YEAST", "protein_name": "Phosphopantothenate--cysteine ligase CAB2", "refseq_ac": "NP_012183", "refseq_name": "phosphopantothenate--cysteine ligase CAB2", "gene_name": "CAB2", "gene_names_uniprotkb": "CAB2", "gene_names_refseq": "CAB2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40506", "url": "https://www.uniprot.org/uniprotkb/P40506" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001345", "url": "https://www.yeastgenome.org/locus/S000001345", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QSGDNGKMGANNDTEGTTRT", "down_seq": "PDGKLIVNLDPVPKFLRRLV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001345", "url": "https://www.yeastgenome.org/locus/S000001345" }, { "database": "iPTMnet", "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr248" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40506-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P40506-1", "length": 365, "uniprot_id": "PPCS_YEAST", "protein_name": "Phosphopantothenate--cysteine ligase CAB2", "refseq_ac": "NP_012183", "refseq_name": "phosphopantothenate--cysteine ligase CAB2", "gene_name": "CAB2", "gene_names_uniprotkb": "CAB2", "gene_names_refseq": "CAB2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40506", "url": "https://www.uniprot.org/uniprotkb/P40506" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001345", "url": "https://www.yeastgenome.org/locus/S000001345", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSGGTTVPLENNTVRFIDNF", "down_seq": "AGTRGASSAEQFLANGYSVI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001345", "url": "https://www.yeastgenome.org/locus/S000001345" }, { "database": "iPTMnet", "id": "P40506", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40506" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser99" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P40506-1.102.102", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40515-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P40515-1", "length": 155, "uniprot_id": "FIS1_YEAST", "protein_name": "Mitochondrial fission 1 protein", "refseq_ac": "NP_012199", "refseq_name": "Fis1p", "gene_name": "FIS1", "gene_names_uniprotkb": "FIS1; MDV2", "gene_names_refseq": "FIS1; MDV2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLYPQQLEILRQQVVSEGGP", "down_seq": "ATIQSRFNYAWGLIKSTDVN", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr36", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40515-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P40515-1", "length": 155, "uniprot_id": "FIS1_YEAST", "protein_name": "Mitochondrial fission 1 protein", "refseq_ac": "NP_012199", "refseq_name": "Fis1p", "gene_name": "FIS1", "gene_names_uniprotkb": "FIS1; MDV2", "gene_names_refseq": "FIS1; MDV2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The WD repeat protein, Mdv1p, functions as a molecular adaptor by interacting with Dnm1p and Fis1p during mitochondrial fission.", "journal": "The Journal of cell biology", "date": "2002-08-05", "authors": "Tieu Quinton, Okreglak Voytek, Naylor Kari, Nunnari Jodi", "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" } ], "reference": [ { "type": "PubMed", "id": "12163467", "url": "https://glygen.org/publication/PubMed/12163467" } ] } ], "crossref": [ { "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12163467", "url": "https://glygen.org/publication/PubMed/12163467", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LGVKILTDIYKEAESRRREC", "down_seq": "YYLTIGCYKLGEYSMAKRYV", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "P", "comment": "In fis1-L80P; no interaction with MDV1; mitochondrial fission is blocked; DNM1 assembly at punctate structures normal as in wild-type.", "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" }, { "database": "PubMed", "id": "12163467", "url": "https://glygen.org/publication/PubMed/12163467" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40515-1.69.69", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40515-1.74.74", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40515-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P40515-1", "length": 155, "uniprot_id": "FIS1_YEAST", "protein_name": "Mitochondrial fission 1 protein", "refseq_ac": "NP_012199", "refseq_name": "Fis1p", "gene_name": "FIS1", "gene_names_uniprotkb": "FIS1; MDV2", "gene_names_refseq": "FIS1; MDV2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001327", "url": "https://www.yeastgenome.org/locus/S000001327", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "M", "down_seq": "KVDFWPTLKDAYEPLYPQQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001327", "url": "https://www.yeastgenome.org/locus/S000001327" }, { "database": "iPTMnet", "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr2" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40515-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P40515-1", "length": 155, "uniprot_id": "FIS1_YEAST", "protein_name": "Mitochondrial fission 1 protein", "refseq_ac": "NP_012199", "refseq_name": "Fis1p", "gene_name": "FIS1", "gene_names_uniprotkb": "FIS1; MDV2", "gene_names_refseq": "FIS1; MDV2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] } ], "crossref": [ { "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LIKSTDVNDERLGVKILTDI", "down_seq": "KEAESRRRECLYYLTIGCYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Tyr69" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40515-1.74.74", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40515-1.80.80", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40515-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P40515-1", "length": 155, "uniprot_id": "FIS1_YEAST", "protein_name": "Mitochondrial fission 1 protein", "refseq_ac": "NP_012199", "refseq_name": "Fis1p", "gene_name": "FIS1", "gene_names_uniprotkb": "FIS1; MDV2", "gene_names_refseq": "FIS1; MDV2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40515", "url": "https://www.uniprot.org/uniprotkb/P40515" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] } ], "crossref": [ { "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DVNDERLGVKILTDIYKEAE", "down_seq": "RRRECLYYLTIGCYKLGEYS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40515", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40515" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser74" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "74", "end_pos": "74" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40515-1.69.69", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40515-1.80.80", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40559-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P40559-1", "length": 946, "uniprot_id": "INP51_YEAST", "protein_name": "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase INP51", "refseq_ac": "NP_012264", "refseq_name": "phosphoinositide 5-phosphatase INP51", "gene_name": "INP51", "gene_names_uniprotkb": "INP51; SJL1; YIA2C", "gene_names_refseq": "INP51; SJL1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40559", "url": "https://www.uniprot.org/uniprotkb/P40559" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000001264", "url": "https://www.yeastgenome.org/locus/S000001264", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CLSFQRLRSIPGASSQQRQL", "down_seq": "KTPSVTIKSYPDTDLSSDSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001264", "url": "https://www.yeastgenome.org/locus/S000001264" }, { "database": "iPTMnet", "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser40" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "40", "end_pos": "40" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "840", "end_pos": "840" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40559-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "P40559-1", "length": 946, "uniprot_id": "INP51_YEAST", "protein_name": "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase INP51", "refseq_ac": "NP_012264", "refseq_name": "phosphoinositide 5-phosphatase INP51", "gene_name": "INP51", "gene_names_uniprotkb": "INP51; SJL1; YIA2C", "gene_names_refseq": "INP51; SJL1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40559", "url": "https://www.uniprot.org/uniprotkb/P40559" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000001264", "url": "https://www.yeastgenome.org/locus/S000001264", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TKVYSKLFGSRVRLYDPLHI", "down_seq": "ISQYLKQLRSKYTFEKDISI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001264", "url": "https://www.yeastgenome.org/locus/S000001264" }, { "database": "iPTMnet", "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Tyr509" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "40", "end_pos": "40" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "840", "end_pos": "840" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40559-1.840.840", "start_pos": 840, "end_pos": 840, "uniprot_canonical_ac": "P40559-1", "length": 946, "uniprot_id": "INP51_YEAST", "protein_name": "Phosphatidylinositol 4,5-bisphosphate 5-phosphatase INP51", "refseq_ac": "NP_012264", "refseq_name": "phosphoinositide 5-phosphatase INP51", "gene_name": "INP51", "gene_names_uniprotkb": "INP51; SJL1; YIA2C", "gene_names_refseq": "INP51; SJL1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40559", "url": "https://www.uniprot.org/uniprotkb/P40559" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "FRARVTVVDEQKKTTLGTQI", "down_seq": "EKIMERLEGLDDDEKIAVLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40559", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40559" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Tyr840" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "40", "end_pos": "40" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "840", "end_pos": "840" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLLYDRNTGTPKGYGYIEFE", "down_seq": "PAYREKALQLNGGELKGKKI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" }, { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser114" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMAYPNPDTFPYYPPYPPNQ", "down_seq": "PNQNFGYNKNNYYRSPYNNK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" }, { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser186" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P40561-1.199.199", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PPYPPNQSPNQNFGYNKNNY", "down_seq": "RSPYNNKNRTFQKKHFNSAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" } ], "site_lbl": "Tyr199" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40561-1.186.186", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] } ], "crossref": [ { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NRTFQKKHFNSAKDSTKNIR", "down_seq": "TSQKPVVMPSDNVKSSTQEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser227" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40561-1.229.229", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TFQKKHFNSAKDSTKNIRST", "down_seq": "QKPVVMPSDNVKSSTQEKDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser229" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40561-1.227.227", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "QEEKVDAKATLKTEISNNKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" }, { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNNKKNDKQELELDELVGKL", "down_seq": "IEGTPQVSQKLSKEEKHAHQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser38" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40561-1.42.42", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40561-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P40561-1", "length": 250, "uniprot_id": "SGN1_YEAST", "protein_name": "RNA-binding protein SGN1", "refseq_ac": "NP_012266", "refseq_name": "Sgn1p", "gene_name": "SGN1", "gene_names_uniprotkb": "SGN1; RBP29; YIB1C", "gene_names_refseq": "RBP1; RBP29; SGN1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40561", "url": "https://www.uniprot.org/uniprotkb/P40561" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KNDKQELELDELVGKLSIEG", "down_seq": "PQVSQKLSKEEKHAHQLEAD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001440", "url": "https://www.yeastgenome.org/locus/S000001440" }, { "database": "iPTMnet", "id": "P40561", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40561" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr42" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40561-1.38.38", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40693", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693" }, { "database": "O-GlcNAc Atlas", "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "STQDSKAQTLNSNPEILLRK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser2", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40693", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40693" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40693-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40693-1.3.3", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40693-1.4.4", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40693-1.7.7", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40693-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40693-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40693", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693" }, { "database": "O-GlcNAc Atlas", "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MS", "down_seq": "TQDSKAQTLNSNPEILLRKR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser3", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40693", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40693" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P40693-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40693-1.2.2", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40693-1.4.4", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40693-1.7.7", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40693-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40693-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40693", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693" }, { "database": "O-GlcNAc Atlas", "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSS", "down_seq": "QDSKAQTLNSNPEILLRKRR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr4", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40693", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40693" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40693-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40693-1.2.2", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40693-1.3.3", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40693-1.7.7", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40693-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40693-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40693", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693" }, { "database": "O-GlcNAc Atlas", "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSSTQD", "down_seq": "KAQTLNSNPEILLRKRRNAD", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser7", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40693", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40693" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40693-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40693-1.2.2", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40693-1.3.3", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40693-1.4.4", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40693-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40693-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40693", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693" }, { "database": "O-GlcNAc Atlas", "id": "P40693", "url": "https://oglcnac.org/atlas/detail/P40693" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40693", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40693" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40693-1.2.2", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40693-1.3.3", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40693-1.4.4", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40693-1.7.7", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40693-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40693-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASGKDFILKITEKANGAEEN", "down_seq": "VDLEETEEEEDDGLIREKTT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser114" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P40693-1.120.120", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSSTQDSKAQ", "down_seq": "LNSNPEILLRKRRNADRTRI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr11" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40693-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40693-1.2.2", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40693-1.3.3", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40693-1.4.4", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40693-1.7.7", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40693-1.14.14", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Asc1p/RACK1 Connects Ribosomes to Eukaryotic Phosphosignaling.", "journal": "Molecular and cellular biology", "date": "2017-02-01", "authors": "Schmitt Kerstin, Smolinski Nadine, Neumann Piotr, Schmaul Samantha, Hofer-Pretz Verena, Braus Gerhard H, Valerius Oliver", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "27821475", "url": "https://glygen.org/publication/PubMed/27821475" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27821475", "url": "https://glygen.org/publication/PubMed/27821475", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ILKITEKANGAEENSVDLEE", "down_seq": "EEEEDDGLIREKTTYDGKPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "27821475", "url": "https://glygen.org/publication/PubMed/27821475" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr120" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40693-1.114.114", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSSTQDSKAQTLN", "down_seq": "NPEILLRKRRNADRTRIERQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser14" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40693-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40693-1.2.2", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40693-1.3.3", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40693-1.4.4", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40693-1.7.7", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40693-1.11.11", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.278.278", "start_pos": 278, "end_pos": 278, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A proteome-wide analysis of kinase-substrate network in the DNA damage response.", "journal": "The Journal of biological chemistry", "date": "2010-04-23", "authors": "Chen Sheng-hong, Albuquerque Claudio P, Liang Jason, Suhandynata Raymond T, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GESFSVCNFFLQPFKLNREV", "down_seq": "GFGSLNRLRKIKQREAESRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20190278", "url": "https://glygen.org/publication/PubMed/20190278" }, { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser278" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P40693-1.282.282", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVCNFFLQPFKLNREVSGFG", "down_seq": "LNRLRKIKQREAESRTRQFS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser282" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P40693-1.278.278", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KREEQIKKKRSNKNKFVRAE", "down_seq": "IVAKTLATSREKERIKRVSI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser60" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P40693-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40693-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P40693-1", "length": 322, "uniprot_id": "RLP7_YEAST", "protein_name": "Ribosome biogenesis protein RLP7", "refseq_ac": "NP_014396", "refseq_name": "Rlp7p", "gene_name": "RLP7", "gene_names_uniprotkb": "RLP7; N2014; RPL7", "gene_names_refseq": "RLP7; RPL7", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40693", "url": "https://www.uniprot.org/uniprotkb/P40693" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESIVAKTLATSREKERIKRV", "down_seq": "ILEDKKAKNETQHIASGKDF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004947", "url": "https://www.yeastgenome.org/locus/S000004947" }, { "database": "iPTMnet", "id": "P40693", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40693" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser79" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "2", "end_pos": "2" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "7", "end_pos": "7" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40693-1.60.60", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40956", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40956" }, { "database": "O-GlcNAc Atlas", "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AHGNINRAIDYLEKSSSSRN", "down_seq": "VSAAATTSTPPLPRRRATTS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser240", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40956", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40956" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser240" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40956-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40956-1.248.248", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40956-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40956", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40956" }, { "database": "O-GlcNAc Atlas", "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNINRAIDYLEKSSSSRNSV", "down_seq": "AAATTSTPPLPRRRATTSGP", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser242", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40956", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40956" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser242" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40956-1.240.240", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.248.248", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40956-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40956", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40956" }, { "database": "O-GlcNAc Atlas", "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IDYLEKSSSSRNSVSAAATT", "down_seq": "TPPLPRRRATTSGPQPAIFD", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser248", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40956", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P40956" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ], "site_lbl": "Ser248" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40956-1.240.240", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40956-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40956-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P40956", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40956" }, { "database": "O-GlcNAc Atlas", "id": "P40956", "url": "https://oglcnac.org/atlas/detail/P40956" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40956", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P40956", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P40956" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P40956-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.6.6", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40956-1.7.7", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RYDEIKPEDFGSRMDDFDGE", "down_seq": "DRFDERNRSRSRSRSHSFYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser153" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P40956-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DFDGESDRFDERNRSRSRSR", "down_seq": "HSFYKGGHNRSDYGGSRDSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser168" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40956-1.153.153", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.", "journal": "Nature biotechnology", "date": "2002-03", "authors": "Ficarro Scott B, McCleland Mark L, Stukenberg P Todd, Burke Daniel J, Ross Mark M, Shabanowitz Jeffrey, Hunt Donald F, White Forest M", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DGESDRFDERNRSRSRSRSH", "down_seq": "FYKGGHNRSDYGGSRDSFQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser170" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40956-1.153.153", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40956-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RNRSRSRSRSHSFYKGGHNR", "down_seq": "DYGGSRDSFQSSGSRYSRQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser179" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P40956-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RSRSRSRSHSFYKGGHNRSD", "down_seq": "GGSRDSFQSSGSRYSRQLAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Tyr181" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P40956-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRSRSHSFYKGGHNRSDYGG", "down_seq": "RDSFQSSGSRYSRQLAELKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser184" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40956-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSHSFYKGGHNRSDYGGSRD", "down_seq": "FQSSGSRYSRQLAELKDMGF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser187" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P40956-1.168.168", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SFYKGGHNRSDYGGSRDSFQ", "down_seq": "SGSRYSRQLAELKDMGFGDT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser190" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P40956-1.170.170", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FYKGGHNRSDYGGSRDSFQS", "down_seq": "GSRYSRQLAELKDMGFGDTN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser191" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KGGHNRSDYGGSRDSFQSSG", "down_seq": "RYSRQLAELKDMGFGDTNKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser193" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40956-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HNRSDYGGSRDSFQSSGSRY", "down_seq": "RQLAELKDMGFGDTNKNLDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser196" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40956-1.179.179", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P40956-1.181.181", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P40956-1.184.184", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40956-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P40956-1.190.190", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P40956-1.191.191", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40956-1.193.193", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLAELKDMGFGDTNKNLDAL", "down_seq": "SAHGNINRAIDYLEKSSSSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser218" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LDALSSAHGNINRAIDYLEK", "down_seq": "SSSRNSVSAAATTSTPPLPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser234" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P40956-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.240.240", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P40956-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40956-1.248.248", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P40956-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DALSSAHGNINRAIDYLEKS", "down_seq": "SSRNSVSAAATTSTPPLPRR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" } ], "site_lbl": "Ser235" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P40956-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40956-1.240.240", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40956-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40956-1.248.248", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P40956-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALSSAHGNINRAIDYLEKSS", "down_seq": "SRNSVSAAATTSTPPLPRRR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser236" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P40956-1.218.218", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P40956-1.240.240", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P40956-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P40956-1.248.248", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P40956-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DYLEKSSSSRNSVSAAATTS", "down_seq": "PPLPRRRATTSGPQPAIFDG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr249" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P40956-1.234.234", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P40956-1.235.235", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P40956-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P40956-1.240.240", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40956-1.242.242", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40956-1.248.248", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RRRATTSGPQPAIFDGTNVI", "down_seq": "PDFTSNSASFVQAKPAVFDG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr274" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P40956-1.281.281", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GPQPAIFDGTNVITPDFTSN", "down_seq": "ASFVQAKPAVFDGTLQQYYD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser281" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40956-1.274.274", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MRFR", "down_seq": "SSHSLKHVDRELKELINSSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ], "site_lbl": "Ser5" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40956-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40956-1.6.6", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40956-1.7.7", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MRFRS", "down_seq": "SHSLKHVDRELKELINSSEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P40956-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40956-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P40956-1.7.7", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MRFRSS", "down_seq": "HSLKHVDRELKELINSSENA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser7" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P40956-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40956-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P40956-1.6.6", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40956-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P40956-1", "length": 396, "uniprot_id": "GTS1_YEAST", "protein_name": "Protein GTS1", "refseq_ac": "NP_011334", "refseq_name": "Gts1p", "gene_name": "GTS1", "gene_names_uniprotkb": "GTS1; LSR1", "gene_names_refseq": "FHT1; GTS1; LSR1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40956", "url": "https://www.uniprot.org/uniprotkb/P40956" }, { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNVKSLSMDRWTREDIDELV", "down_seq": "LGGNKGNARFWNPKNVPFPF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40956", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40956" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000003149", "url": "https://www.yeastgenome.org/locus/S000003149" } ], "site_lbl": "Ser90" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "153", "end_pos": "153" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae.", "journal": "Genes & development", "date": "2001-12-01", "authors": "Meijsing S H, Ehrenhofer-Murray A E", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "reference": [ { "type": "PubMed", "id": "11731480", "url": "https://glygen.org/publication/PubMed/11731480" } ] }, { "title": "The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1.", "journal": "Genes & development", "date": "2001-12-01", "authors": "Osada S, Sutton A, Muster N, Brown C E, Yates J R, Sternglanz R, Workman J L", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "reference": [ { "type": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "crossref": [ { "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11731480", "url": "https://glygen.org/publication/PubMed/11731480", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "QLSSVSNSQYWLDTLFVCEY", "down_seq": "FKYTDDQTRFVGHVASCPFQ", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "L", "comment": "Loss of function.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" }, { "database": "PubMed", "id": "11731480", "url": "https://glygen.org/publication/PubMed/11731480" }, { "database": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SKYQLFCQCLCLFTKLYLDN", "down_seq": "SMYFKVDHYEFYIVYETGST", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Abolishes catalytic activity.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ] }, { "sequence_org": "K", "sequence_mut": "Q", "comment": "Abolishes catalytic activity.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ] }, { "sequence_org": "K", "sequence_mut": "R", "comment": "Abolishes catalytic activity.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P40963-1.213.214", "start_pos": 213, "end_pos": 214, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae.", "journal": "Genes & development", "date": "2001-12-01", "authors": "Meijsing S H, Ehrenhofer-Murray A E", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "reference": [ { "type": "PubMed", "id": "11731480", "url": "https://glygen.org/publication/PubMed/11731480" } ] } ], "crossref": [ { "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11731480", "url": "https://glygen.org/publication/PubMed/11731480", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "PP", "start_aa": "P", "up_seq": "FFSKDLVSYQQNNLACILIF", "down_seq": "YQRRGLGLLLIEFSYKLSQL", "mutagenesis": [ { "sequence_org": "PP", "sequence_mut": "AV", "comment": "Loss of function.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" }, { "database": "PubMed", "id": "11731480", "url": "https://glygen.org/publication/PubMed/11731480" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40963-1.216.217", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P40963-1.219.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P40963-1.224.225", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.216.217", "start_pos": 216, "end_pos": 217, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1.", "journal": "Genes & development", "date": "2001-12-01", "authors": "Osada S, Sutton A, Muster N, Brown C E, Yates J R, Sternglanz R, Workman J L", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "reference": [ { "type": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "crossref": [ { "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "QR", "start_aa": "Q", "up_seq": "KDLVSYQQNNLACILIFPPY", "down_seq": "RGLGLLLIEFSYKLSQLEGV", "mutagenesis": [ { "sequence_org": "QR", "sequence_mut": "AA", "comment": "Abolishes silencing activity.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" }, { "database": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40963-1.213.214", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P40963-1.219.221", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P40963-1.224.225", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.219.221", "start_pos": 219, "end_pos": 221, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1.", "journal": "Genes & development", "date": "2001-12-01", "authors": "Osada S, Sutton A, Muster N, Brown C E, Yates J R, Sternglanz R, Workman J L", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "reference": [ { "type": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "crossref": [ { "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "GLG", "start_aa": "G", "up_seq": "VSYQQNNLACILIFPPYQRR", "down_seq": "LLLIEFSYKLSQLEGVISGP", "mutagenesis": [ { "sequence_org": "GLG", "sequence_mut": "AAA", "comment": "Does not affect silencing activity.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" }, { "database": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P40963-1.213.214", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P40963-1.216.217", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P40963-1.224.225", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.224.225", "start_pos": 224, "end_pos": 225, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1.", "journal": "Genes & development", "date": "2001-12-01", "authors": "Osada S, Sutton A, Muster N, Brown C E, Yates J R, Sternglanz R, Workman J L", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "reference": [ { "type": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "crossref": [ { "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "LI", "start_aa": "L", "up_seq": "NNLACILIFPPYQRRGLGLL", "down_seq": "EFSYKLSQLEGVISGPEVPL", "mutagenesis": [ { "sequence_org": "LI", "sequence_mut": "AA", "comment": "Does not affect silencing activity.", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" }, { "database": "PubMed", "id": "11731479", "url": "https://glygen.org/publication/PubMed/11731479" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P40963-1.213.214", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P40963-1.216.217", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P40963-1.219.221", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MAR", "down_seq": "LSQSLTATTQKLKGKKNGGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser4" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P40963-1.6.6", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40963-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P40963-1", "length": 338, "uniprot_id": "SAS2_YEAST", "protein_name": "Histone acetyltransferase SAS2", "refseq_ac": "NP_013846", "refseq_name": "histone acetyltransferase", "gene_name": "SAS2", "gene_names_uniprotkb": "SAS2; ESO1; YM9553.03C", "gene_names_refseq": "KAT8; SAS2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P40963", "url": "https://www.uniprot.org/uniprotkb/P40963" }, { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004734", "url": "https://www.yeastgenome.org/locus/S000004734", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MARSL", "down_seq": "QSLTATTQKLKGKKNGGKGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40963", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40963" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000004734", "url": "https://www.yeastgenome.org/locus/S000004734" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "213", "end_pos": "214" }, { "start_pos": "216", "end_pos": "217" }, { "start_pos": "219", "end_pos": "221" }, { "start_pos": "224", "end_pos": "225" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "4", "end_pos": "4" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P40963-1.4.4", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P40968-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "P40968-1", "length": 455, "uniprot_id": "PRP17_YEAST", "protein_name": "Pre-mRNA-processing factor 17", "refseq_ac": "NP_010652", "refseq_name": "Cdc40p", "gene_name": "CDC40", "gene_names_uniprotkb": "CDC40; D9481.11; PRP17; SLU4; XRS2", "gene_names_refseq": "CDC40; PRP17; SLT15; SLU4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P40968", "url": "https://www.uniprot.org/uniprotkb/P40968" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P40968", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40968" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P40968", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40968", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002772", "url": "https://www.yeastgenome.org/locus/S000002772", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DLREERISFRCYLPKKVIRN", "down_seq": "PGHPEGTTALKFLPKTGHLI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P40968", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P40968" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000002772", "url": "https://www.yeastgenome.org/locus/S000002772" } ], "site_lbl": "Tyr158" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "158", "end_pos": "158" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "RTG-dependent mitochondria to nucleus signaling is negatively regulated by the seven WD-repeat protein Lst8p.", "journal": "The EMBO journal", "date": "2001-12-17", "authors": "Liu Z, Sekito T, Epstein C B, Butow R A", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "reference": [ { "type": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "crossref": [ { "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PVNEVVIHPNQGELISCDRD", "down_seq": "NIRIWDLGENQCTHQLTPED", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "D", "comment": "In LST8-3; abolishes repression of RTG1-RTG3-dependent gene expression.", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" }, { "database": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P41318-1.146.146", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "RTG-dependent mitochondria to nucleus signaling is negatively regulated by the seven WD-repeat protein Lst8p.", "journal": "The EMBO journal", "date": "2001-12-17", "authors": "Liu Z, Sekito T, Epstein C B, Butow R A", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "reference": [ { "type": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "crossref": [ { "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PNQGELISCDRDGNIRIWDL", "down_seq": "ENQCTHQLTPEDDTSLQSLS", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "E", "comment": "In LST8-2; abolishes repression of RTG1-RTG3-dependent gene expression.", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" }, { "database": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41318-1.138.138", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "RTG-dependent mitochondria to nucleus signaling is negatively regulated by the seven WD-repeat protein Lst8p.", "journal": "The EMBO journal", "date": "2001-12-17", "authors": "Liu Z, Sekito T, Epstein C B, Butow R A", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "reference": [ { "type": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "crossref": [ { "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "THQLTPEDDTSLQSLSMASD", "down_seq": "SMLAAANTKGNCYVWEMPNH", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "E", "comment": "In LST8-5; abolishes repression of RTG1-RTG3-dependent gene expression.", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" }, { "database": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P41318-1.181.181", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "RTG-dependent mitochondria to nucleus signaling is negatively regulated by the seven WD-repeat protein Lst8p.", "journal": "The EMBO journal", "date": "2001-12-17", "authors": "Liu Z, Sekito T, Epstein C B, Butow R A", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "reference": [ { "type": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "crossref": [ { "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SLQSLSMASDGSMLAAANTK", "down_seq": "NCYVWEMPNHTDASHLKPVT", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "E", "comment": "In LST8-4; abolishes repression of RTG1-RTG3-dependent gene expression.", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" }, { "database": "PubMed", "id": "11742997", "url": "https://glygen.org/publication/PubMed/11742997" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P41318-1.171.171", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Control of amino acid permease sorting in the late secretory pathway of Saccharomyces cerevisiae by SEC13, LST4, LST7 and LST8.", "journal": "Genetics", "date": "1997", "authors": "Roberg KJ, Bickel S, Rowley N, Kaiser CA", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "reference": [ { "type": "PubMed", "id": "9409822", "url": "https://glygen.org/publication/PubMed/9409822" } ] } ], "crossref": [ { "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9409822", "url": "https://glygen.org/publication/PubMed/9409822", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "STREIVRQYGGHHKGAVCVA", "down_seq": "NDV", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "S", "comment": "In LST8-1; abolishes repression of RTG2- and RTG1-RTG3-dependent gene expression.", "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" }, { "database": "PubMed", "id": "9409822", "url": "https://glygen.org/publication/PubMed/9409822" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41318", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41318" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004951", "url": "https://www.yeastgenome.org/locus/S000004951", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41318", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41318", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DNRWMVTSSEDGTIKVWDVR", "down_seq": "PSIPRNYKHNAPVNEVVIHP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004951", "url": "https://www.yeastgenome.org/locus/S000004951" }, { "database": "iPTMnet", "id": "P41318", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41318" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser106" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41318-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "P41318-1", "length": 303, "uniprot_id": "LST8_YEAST", "protein_name": "Target of rapamycin complex subunit LST8", "refseq_ac": "NP_014392", "refseq_name": "TOR complex subunit LST8", "gene_name": "LST8", "gene_names_uniprotkb": "LST8; N2005", "gene_names_refseq": "LST8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41318", "url": "https://www.uniprot.org/uniprotkb/P41318" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41318", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41318" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000004951", "url": "https://www.yeastgenome.org/locus/S000004951", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41318", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41318", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EMPNHTDASHLKPVTKFRAH", "down_seq": "TYITRILLSSDVKHLATCSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004951", "url": "https://www.yeastgenome.org/locus/S000004951" }, { "database": "iPTMnet", "id": "P41318", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41318" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser207" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "138", "end_pos": "138" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "300", "end_pos": "300" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "207", "end_pos": "207" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41543-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P41543-1", "length": 476, "uniprot_id": "OST1_YEAST", "protein_name": "Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1", "refseq_ac": "NP_012532", "refseq_name": "dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1", "gene_name": "OST1", "gene_names_uniprotkb": "OST1; J1404; NLT1", "gene_names_refseq": "NLT1; OST1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "PRU00498", "url": "https://prosite.expasy.org/rule/PRU00498", "database": "PROSITE-ProRule", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MRQVWFSWIVGLFLCFF", "down_seq": "VSSAAQYEPPATWENVDYKR", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn18", "evidence": [ { "id": "P41543", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "id": "PRU00498", "database": "PROSITE-ProRule", "url": "https://prosite.expasy.org/rule/PRU00498" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P41543-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P41543-1", "length": 476, "uniprot_id": "OST1_YEAST", "protein_name": "Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1", "refseq_ac": "NP_012532", "refseq_name": "dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1", "gene_name": "OST1", "gene_names_uniprotkb": "OST1; J1404; NLT1", "gene_names_refseq": "NLT1; OST1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "PRU00498", "url": "https://prosite.expasy.org/rule/PRU00498", "database": "PROSITE-ProRule", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KANGNSFEFGPWEDIPRFSS", "down_seq": "ETLAIVYSHNAPLNQVVNLR", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn217", "evidence": [ { "id": "P41543", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "id": "PRU00498", "database": "PROSITE-ProRule", "url": "https://prosite.expasy.org/rule/PRU00498" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P41543-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "P41543-1", "length": 476, "uniprot_id": "OST1_YEAST", "protein_name": "Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1", "refseq_ac": "NP_012532", "refseq_name": "dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1", "gene_name": "OST1", "gene_names_uniprotkb": "OST1; J1404; NLT1", "gene_names_refseq": "NLT1; OST1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.", "journal": "Science (New York, N.Y.)", "date": "2018-02-02", "authors": "Wild Rebekka, Kowal Julia, Eyring Jillianne, Ngwa Elsy M, Aebi Markus, Locher Kaspar P", "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "reference": [ { "type": "PubMed", "id": "29301962", "url": "https://glygen.org/publication/PubMed/29301962" } ] } ], "crossref": [ { "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29301962", "url": "https://glygen.org/publication/PubMed/29301962", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AERDHFFIRPRFPIFGGWNY", "down_seq": "FTVGWTNKLSDFLHVSSGSD", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn336", "evidence": [ { "id": "P41543", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "id": "29301962", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29301962" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41543-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "P41543-1", "length": 476, "uniprot_id": "OST1_YEAST", "protein_name": "Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1", "refseq_ac": "NP_012532", "refseq_name": "dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1", "gene_name": "OST1", "gene_names_uniprotkb": "OST1; J1404; NLT1", "gene_names_refseq": "NLT1; OST1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.", "journal": "Science (New York, N.Y.)", "date": "2018-02-02", "authors": "Wild Rebekka, Kowal Julia, Eyring Jillianne, Ngwa Elsy M, Aebi Markus, Locher Kaspar P", "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "reference": [ { "type": "PubMed", "id": "29301962", "url": "https://glygen.org/publication/PubMed/29301962" } ] } ], "crossref": [ { "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "29301962", "url": "https://glygen.org/publication/PubMed/29301962", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7OCI", "url": "https://www.rcsb.org/structure/7OCI", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7OCI|A|400", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SVFLPEGAEIFDIDSPVPFT", "down_seq": "VSIETQKSYFDLNKGHVKLT", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7OCI&bu=0&command=select+.A:400;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn400", "evidence": [ { "id": "P41543", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "id": "29301962", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29301962" }, { "id": "7OCI", "database": "PDB", "url": "https://www.rcsb.org/structure/7OCI" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41543-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P41543-1", "length": 476, "uniprot_id": "OST1_YEAST", "protein_name": "Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1", "refseq_ac": "NP_012532", "refseq_name": "dolichyl-diphosphooligosaccharide--protein glycotransferase subunit OST1", "gene_name": "OST1", "gene_names_uniprotkb": "OST1; J1404; NLT1", "gene_names_refseq": "NLT1; OST1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P41543", "url": "https://www.uniprot.org/uniprotkb/P41543", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "PRU00498", "url": "https://prosite.expasy.org/rule/PRU00498", "database": "PROSITE-ProRule", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SFFSAYFTNEATFLNSQLLA", "down_seq": "STTAPGDDGESEIRYGIIQF", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn99", "evidence": [ { "id": "P41543", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P41543#ptm_processing" }, { "id": "PRU00498", "database": "PROSITE-ProRule", "url": "https://prosite.expasy.org/rule/PRU00498" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "99", "end_pos": "99" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P41813-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLEVSIGRNTDPLNSALQEN", "down_seq": "DGVKNSYRVNIDLGPAKVVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser100" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNQQIKGFKLYGSGGNAPFG", "down_seq": "GANLGPSEQGIFNNNNNSKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser250" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INPNYTASTTTSNTINPQAA", "down_seq": "PQGPPNTIIAANFVDSYKSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser298" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.440.440", "start_pos": 440, "end_pos": 440, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YQQEFLNKWNTGKVGKIRRG", "down_seq": "SVARQLQLHMAKFNSLPMEM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser440" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P41813-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41813-1.455.455", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.441.441", "start_pos": 441, "end_pos": 441, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proc. Natl. Acad. Sci. U.S.A.", "date": "2007", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQEFLNKWNTGKVGKIRRGS", "down_seq": "VARQLQLHMAKFNSLPMEMD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser441" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P41813-1.440.440", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41813-1.455.455", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.455.455", "start_pos": 455, "end_pos": 455, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIRRGSSVARQLQLHMAKFN", "down_seq": "LPMEMDYRLSLNMAQPPKRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" } ], "site_lbl": "Ser455" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P41813-1.440.440", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41813-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41813-1.462.462", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VARQLQLHMAKFNSLPMEMD", "down_seq": "RLSLNMAQPPKRQLQSHNVL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" } ], "site_lbl": "Tyr462" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P41813-1.455.455", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNNIIEGFVQHVPSKGNLPA", "down_seq": "QQSQPPVSHQNQSQQPPPQE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser506" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P41813-1.509.509", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IIEGFVQHVPSKGNLPASQQ", "down_seq": "QPPVSHQNQSQQPPPQEQRQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser509" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41813-1.506.506", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.611.611", "start_pos": 611, "end_pos": 611, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NNALVSFTNACANSKIINNI", "down_seq": "DSADKSTNNNGGTKMNLPAI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser611" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P41813-1.613.613", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.613.613", "start_pos": 613, "end_pos": 613, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ALVSFTNACANSKIINNISD", "down_seq": "ADKSTNNNGGTKMNLPAIST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser613" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P41813-1.611.611", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.674.674", "start_pos": 674, "end_pos": 674, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSVPQTGTTTSSLAANSLRL", "down_seq": "QPYDTLLRSPTKAFHITAME", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser674" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P41813-1.679.679", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41813-1.683.683", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41813-1.685.685", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.679.679", "start_pos": 679, "end_pos": 679, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TGTTTSSLAANSLRLSQPYD", "down_seq": "LLRSPTKAFHITAMEAYTPE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr679" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P41813-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41813-1.683.683", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41813-1.685.685", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41813-1.697.697", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.683.683", "start_pos": 683, "end_pos": 683, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Regulation of cell cycle-specific gene expression through cyclin-dependent kinase-mediated phosphorylation of the forkhead transcription factor Fkh2p.", "journal": "Molecular and cellular biology", "date": "2004-11", "authors": "Pic-Taylor Aline, Darieva Zoulfia, Morgan Brian A, Sharrocks Andrew D", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "15509804", "url": "https://glygen.org/publication/PubMed/15509804" } ] }, { "title": "A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle.", "journal": "NPJ systems biology and applications", "date": "2017", "authors": "Linke Christian, Chasapi Anastasia, Gonz\u00e1lez-Novo Alberto, Al Sawad Istabrak, Tognetti Silvia, Klipp Edda, Loog Mart, Krobitsch Sylvia, Posas Francesc, Xenarios Ioannis, Barberis Matteo", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "28649434", "url": "https://glygen.org/publication/PubMed/28649434" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15509804", "url": "https://glygen.org/publication/PubMed/15509804", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28649434", "url": "https://glygen.org/publication/PubMed/28649434", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSSLAANSLRLSQPYDTLLR", "down_seq": "PTKAFHITAMEAYTPERGSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "15509804", "url": "https://glygen.org/publication/PubMed/15509804" } ], "site_lbl": "Ser683" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "28649434", "url": "https://glygen.org/publication/PubMed/28649434" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser683" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P41813-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41813-1.679.679", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41813-1.685.685", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41813-1.697.697", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.685.685", "start_pos": 685, "end_pos": 685, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SLAANSLRLSQPYDTLLRSP", "down_seq": "KAFHITAMEAYTPERGSANR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr685" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41813-1.674.674", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41813-1.679.679", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41813-1.683.683", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41813-1.697.697", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.697.697", "start_pos": 697, "end_pos": 697, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Regulation of cell cycle-specific gene expression through cyclin-dependent kinase-mediated phosphorylation of the forkhead transcription factor Fkh2p.", "journal": "Molecular and cellular biology", "date": "2004-11", "authors": "Pic-Taylor Aline, Darieva Zoulfia, Morgan Brian A, Sharrocks Andrew D", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "15509804", "url": "https://glygen.org/publication/PubMed/15509804" } ] }, { "title": "A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle.", "journal": "NPJ systems biology and applications", "date": "2017", "authors": "Linke Christian, Chasapi Anastasia, Gonz\u00e1lez-Novo Alberto, Al Sawad Istabrak, Tognetti Silvia, Klipp Edda, Loog Mart, Krobitsch Sylvia, Posas Francesc, Xenarios Ioannis, Barberis Matteo", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "28649434", "url": "https://glygen.org/publication/PubMed/28649434" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15509804", "url": "https://glygen.org/publication/PubMed/15509804", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28649434", "url": "https://glygen.org/publication/PubMed/28649434", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YDTLLRSPTKAFHITAMEAY", "down_seq": "PERGSANRARSPLHSNSNNT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "15509804", "url": "https://glygen.org/publication/PubMed/15509804" } ], "site_lbl": "Thr697" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "28649434", "url": "https://glygen.org/publication/PubMed/28649434" } ], "site_lbl": "Thr697" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41813-1.679.679", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41813-1.683.683", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P41813-1.685.685", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41813-1.708.708", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41813-1.712.712", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41813-1.714.714", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.708.708", "start_pos": 708, "end_pos": 708, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FHITAMEAYTPERGSANRAR", "down_seq": "PLHSNSNNTNNNGANNSNLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser708" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ], "site_lbl": "Ser708" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser708" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41813-1.697.697", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41813-1.712.712", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41813-1.714.714", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41813-1.725.725", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.712.712", "start_pos": 712, "end_pos": 712, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AMEAYTPERGSANRARSPLH", "down_seq": "NSNNTNNNGANNSNLQTSGM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser712" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P41813-1.697.697", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41813-1.708.708", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41813-1.714.714", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41813-1.725.725", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41813-1.729.729", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.714.714", "start_pos": 714, "end_pos": 714, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAYTPERGSANRARSPLHSN", "down_seq": "NNTNNNGANNSNLQTSGMEN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser714" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41813-1.697.697", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41813-1.708.708", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41813-1.712.712", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41813-1.725.725", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41813-1.729.729", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.725.725", "start_pos": 725, "end_pos": 725, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RARSPLHSNSNNTNNNGANN", "down_seq": "NLQTSGMENKQTGLVLDSNV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser725" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41813-1.708.708", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P41813-1.712.712", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P41813-1.714.714", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41813-1.729.729", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.729.729", "start_pos": 729, "end_pos": 729, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLHSNSNNTNNNGANNSNLQ", "down_seq": "SGMENKQTGLVLDSNVLKSM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr729" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41813-1.712.712", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P41813-1.714.714", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41813-1.725.725", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41813-1.748.748", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.748.748", "start_pos": 748, "end_pos": 748, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QTSGMENKQTGLVLDSNVLK", "down_seq": "MESNNDNRRLTPSTSKSQNV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser748" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41813-1.729.729", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41813-1.759.759", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41813-1.765.765", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.759.759", "start_pos": 759, "end_pos": 759, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LVLDSNVLKSMESNNDNRRL", "down_seq": "PSTSKSQNVKSSPGVWNLLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr759" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41813-1.748.748", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41813-1.765.765", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.765.765", "start_pos": 765, "end_pos": 765, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VLKSMESNNDNRRLTPSTSK", "down_seq": "QNVKSSPGVWNLLQFSSTNN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser765" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41813-1.748.748", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41813-1.759.759", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41813-1.781.781", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41813-1.782.782", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.781.781", "start_pos": 781, "end_pos": 781, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSKSQNVKSSPGVWNLLQF", "down_seq": "STNNTPAADSGGNKRGFSIN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser781" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41813-1.765.765", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41813-1.782.782", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41813-1.799.799", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.782.782", "start_pos": 782, "end_pos": 782, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSKSQNVKSSPGVWNLLQFS", "down_seq": "TNNTPAADSGGNKRGFSINP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser782" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41813-1.765.765", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41813-1.781.781", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41813-1.799.799", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.799.799", "start_pos": 799, "end_pos": 799, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QFSSTNNTPAADSGGNKRGF", "down_seq": "INPDIKAKENENATSEKDSD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser799" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41813-1.781.781", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P41813-1.782.782", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.813.813", "start_pos": 813, "end_pos": 813, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GNKRGFSINPDIKAKENENA", "down_seq": "SEKDSDSNSNDLETKDINSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr813" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P41813-1.799.799", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41813-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41813-1.822.822", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41813-1.832.832", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41813-1.833.833", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.814.814", "start_pos": 814, "end_pos": 814, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NKRGFSINPDIKAKENENAT", "down_seq": "EKDSDSNSNDLETKDINSSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ], "site_lbl": "Ser814" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P41813-1.799.799", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41813-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41813-1.822.822", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41813-1.832.832", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41813-1.833.833", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.818.818", "start_pos": 818, "end_pos": 818, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FSINPDIKAKENENATSEKD", "down_seq": "DSNSNDLETKDINSSPLKNQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser818" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41813-1.799.799", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41813-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41813-1.822.822", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41813-1.832.832", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41813-1.833.833", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.820.820", "start_pos": 820, "end_pos": 820, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INPDIKAKENENATSEKDSD", "down_seq": "NSNDLETKDINSSPLKNQGG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ], "site_lbl": "Ser820" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41813-1.822.822", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41813-1.832.832", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41813-1.833.833", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.822.822", "start_pos": 822, "end_pos": 822, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDIKAKENENATSEKDSDSN", "down_seq": "NDLETKDINSSPLKNQGGST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser822" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41813-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41813-1.832.832", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41813-1.833.833", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.832.832", "start_pos": 832, "end_pos": 832, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ATSEKDSDSNSNDLETKDIN", "down_seq": "SPLKNQGGSTANAKELILDT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser832" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P41813-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41813-1.822.822", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41813-1.833.833", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41813-1.833.833", "start_pos": 833, "end_pos": 833, "uniprot_canonical_ac": "P41813-1", "length": 862, "uniprot_id": "FKH2_YEAST", "protein_name": "Fork head protein homolog 2", "refseq_ac": "NP_014331", "refseq_name": "forkhead family transcription factor FKH2", "gene_name": "FKH2", "gene_names_uniprotkb": "FKH2; N2403; YNL2403C", "gene_names_refseq": "FKH2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSEKDSDSNSNDLETKDINS", "down_seq": "PLKNQGGSTANAKELILDTD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser833" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser833" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41813", "url": "https://www.uniprot.org/uniprotkb/P41813" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005012", "url": "https://www.yeastgenome.org/locus/S000005012" }, { "database": "iPTMnet", "id": "P41813", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41813" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser833" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "683", "end_pos": "683" }, { "start_pos": "685", "end_pos": "685" }, { "start_pos": "697", "end_pos": "697" }, { "start_pos": "708", "end_pos": "708" }, { "start_pos": "712", "end_pos": "712" }, { "start_pos": "714", "end_pos": "714" }, { "start_pos": "725", "end_pos": "725" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "759", "end_pos": "759" }, { "start_pos": "765", "end_pos": "765" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "782", "end_pos": "782" }, { "start_pos": "799", "end_pos": "799" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "814", "end_pos": "814" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "832", "end_pos": "832" }, { "start_pos": "833", "end_pos": "833" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41813-1.813.813", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P41813-1.814.814", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P41813-1.818.818", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P41813-1.820.820", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P41813-1.822.822", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41813-1.832.832", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of protein phosphatase-1 and aurora protein kinase suppressors reveals new aspects of regulatory protein function in Saccharomyces cerevisiae.", "journal": "PloS one", "date": "2013", "authors": "Ghosh Anuprita, Cannon John F", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "23894419", "url": "https://glygen.org/publication/PubMed/23894419" } ] }, { "title": "Novel phosphorylation-dependent regulation in an unstructured protein.", "journal": "Proteins", "date": "2020-02", "authors": "Cannon John F", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "31512287", "url": "https://glygen.org/publication/PubMed/31512287" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "Pho85 phosphorylates the Glc7 protein phosphatase regulator Glc8 in vivo.", "journal": "The Journal of biological chemistry", "date": "2003-01-03", "authors": "Tan Yves S H, Morcos Paul A, Cannon John F", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "12407105", "url": "https://glygen.org/publication/PubMed/12407105" } ] } ], "crossref": [ { "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23894419", "url": "https://glygen.org/publication/PubMed/23894419", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "31512287", "url": "https://glygen.org/publication/PubMed/31512287", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12407105", "url": "https://glygen.org/publication/PubMed/12407105", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LAENEITKKQFQDIHIDEPK", "down_seq": "PYQGAVDPHGEYYRVDDDED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by PHO85", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "23894419", "url": "https://glygen.org/publication/PubMed/23894419" }, { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "PubMed", "id": "31512287", "url": "https://glygen.org/publication/PubMed/31512287" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "12407105", "url": "https://glygen.org/publication/PubMed/12407105" } ], "site_lbl": "Thr118" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P41818-1.120.120", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ENEITKKQFQDIHIDEPKTP", "down_seq": "QGAVDPHGEYYRVDDDEDED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" } ], "site_lbl": "Tyr120" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P41818-1.118.118", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MGGILKNPLAL", "down_seq": "PEQLAQQDPETLEEFRRQVY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser12" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEDNSDKKPCQVANDDIDDL", "down_seq": "LGEPEFEIKENKQPDFETND", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser158" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P41818-1.176.176", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DLSLGEPEFEIKENKQPDFE", "down_seq": "NDENDEDSPEARHKKFEEMR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Thr176" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41818-1.158.158", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41818-1.184.184", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FEIKENKQPDFETNDENDED", "down_seq": "PEARHKKFEEMRKKHYDVRA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser184" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41818-1.176.176", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AIFNKKSREALKDEDEDEDD", "down_seq": "TTKEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser224" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SHKRNIPGLDNTKEEGEIIG", "down_seq": "SSTFLPKDTLSLKHEQDMLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr63" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P41818-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41818-1.66.66", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HKRNIPGLDNTKEEGEIIGT", "down_seq": "STFLPKDTLSLKHEQDMLAK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser64" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P41818-1.63.63", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41818-1.66.66", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41818-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P41818-1", "length": 229, "uniprot_id": "GLC8_YEAST", "protein_name": "Protein GLC8", "refseq_ac": "NP_014042", "refseq_name": "PP1-complex regulatory subunit GLC8", "gene_name": "GLC8", "gene_names_uniprotkb": "GLC8; YM9924.03C", "gene_names_refseq": "GLC8", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41818", "url": "https://www.uniprot.org/uniprotkb/P41818" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RNIPGLDNTKEEGEIIGTSS", "down_seq": "FLPKDTLSLKHEQDMLAKMT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000004928", "url": "https://www.yeastgenome.org/locus/S000004928" }, { "database": "iPTMnet", "id": "P41818", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41818" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr66" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41818-1.63.63", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41818-1.64.64", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LNTQNLSQYMNGKLSGDVPV", "down_seq": "SQHARSHSMQSKYSYSKRNS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser111", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P41832-1.112.112", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.117.117", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.119.119", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.122.122", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTQNLSQYMNGKLSGDVPVS", "down_seq": "QHARSHSMQSKYSYSKRNSS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser112", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P41832-1.111.111", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P41832-1.117.117", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.119.119", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.122.122", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1170.1170", "start_pos": 1170, "end_pos": 1170, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKVNKVEPYEQNEDEGLDKK", "down_seq": "LPENSTASAASAFDKAEKDM", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser1170", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1170" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P41832-1.1175.1175", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.1178.1178", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.1181.1181", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1175.1175", "start_pos": 1175, "end_pos": 1175, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VEPYEQNEDEGLDKKSLPEN", "down_seq": "TASAASAFDKAEKDMRQHVE", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser1175", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1175" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P41832-1.1170.1170", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1178.1178", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1181.1181", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1178.1178", "start_pos": 1178, "end_pos": 1178, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YEQNEDEGLDKKSLPENSTA", "down_seq": "AASAFDKAEKDMRQHVENGK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser1178", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41832-1.1170.1170", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1175.1175", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1181.1181", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQYMNGKLSGDVPVSSQHAR", "down_seq": "HSMQSKYSYSKRNSSQASNK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser117", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P41832-1.111.111", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P41832-1.112.112", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.119.119", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P41832-1.122.122", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41832-1.135.135", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1181.1181", "start_pos": 1181, "end_pos": 1181, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NEDEGLDKKSLPENSTASAA", "down_seq": "AFDKAEKDMRQHVENGKQGR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser1181", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1181" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41832-1.1170.1170", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1175.1175", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1178.1178", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YMNGKLSGDVPVSSQHARSH", "down_seq": "MQSKYSYSKRNSSQASNKLT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser119", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41832-1.111.111", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P41832-1.112.112", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.117.117", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.122.122", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.135.135", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKLSGDVPVSSQHARSHSMQ", "down_seq": "KYSYSKRNSSQASNKLTRQH", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser122", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41832-1.111.111", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.112.112", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P41832-1.117.117", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.119.119", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41832-1.135.135", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNELKKMRANTTSSSTASRT", "down_seq": "MASDHHPILTANSSLSSPKS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser244", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41832-1.241.241", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKKMRANTTSSSTASRTSMA", "down_seq": "DHHPILTANSSLSSPKSVLM", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser247", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser247" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P41832-1.241.241", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSTASRTSMASDHHPILTAN", "down_seq": "SLSSPKSVLMTSASSPTSTV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser257", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ], "site_lbl": "Ser257" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41832-1.241.241", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P41832-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STASRTSMASDHHPILTANS", "down_seq": "LSSPKSVLMTSASSPTSTVY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser258", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41832-1.241.241", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41832-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P41832-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.260.260", "start_pos": 260, "end_pos": 260, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASRTSMASDHHPILTANSSL", "down_seq": "SPKSVLMTSASSPTSTVYSN", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser260", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser260" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41832-1.241.241", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P41832-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P41832-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRTSMASDHHPILTANSSLS", "down_seq": "PKSVLMTSASSPTSTVYSNS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser261", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser261" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41832-1.241.241", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P41832-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41832-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLKKQPSLNNIYRGGAENNT", "down_seq": "ASTLPGDRTNRPPIHYVQRI", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser325", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser325" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41832-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.324.324", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.327.327", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.328.328", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKQPSLNNIYRGGAENNTSA", "down_seq": "TLPGDRTNRPPIHYVQRILA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser327", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser327" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.324.324", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.325.325", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.328.328", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" }, { "database": "O-GlcNAc Atlas", "id": "P41832", "url": "https://oglcnac.org/atlas/detail/P41832" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P41832", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P41832" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P41832-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41832-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41832-1.20.20", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1076.1076", "start_pos": 1076, "end_pos": 1076, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSDDESEEIYQDASPTQELR", "down_seq": "EHSELSSGSGPGSFLDALSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1076" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P41832-1.1079.1079", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41832-1.1085.1085", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41832-1.1089.1089", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1079.1079", "start_pos": 1079, "end_pos": 1079, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DESEEIYQDASPTQELRSEH", "down_seq": "ELSSGSGPGSFLDALSQKYG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1079" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41832-1.1076.1076", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1085.1085", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.1089.1089", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1082.1082", "start_pos": 1082, "end_pos": 1082, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEIYQDASPTQELRSEHSEL", "down_seq": "SGSGPGSFLDALSQKYGTGQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1082" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P41832-1.1076.1076", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1079.1079", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1085.1085", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.1089.1089", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1083.1083", "start_pos": 1083, "end_pos": 1083, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIYQDASPTQELRSEHSELS", "down_seq": "GSGPGSFLDALSQKYGTGQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1083" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P41832-1.1076.1076", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.1079.1079", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.1085.1085", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1089.1089", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1085.1085", "start_pos": 1085, "end_pos": 1085, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YQDASPTQELRSEHSELSSG", "down_seq": "GPGSFLDALSQKYGTGQNVT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1085" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P41832-1.1076.1076", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1079.1079", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1089.1089", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1089.1089", "start_pos": 1089, "end_pos": 1089, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPTQELRSEHSELSSGSGPG", "down_seq": "FLDALSQKYGTGQNVTASAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1089" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P41832-1.1076.1076", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.1079.1079", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P41832-1.1082.1082", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1083.1083", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.1085.1085", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1137.1137", "start_pos": 1137, "end_pos": 1137, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGIGPLHSKVEKTFMNRLRK", "down_seq": "TVSSAPYLEELTQKVNKVEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1137" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P41832-1.1138.1138", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1140.1140", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1141.1141", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.1144.1144", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1138.1138", "start_pos": 1138, "end_pos": 1138, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GIGPLHSKVEKTFMNRLRKS", "down_seq": "VSSAPYLEELTQKVNKVEPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr1138" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P41832-1.1137.1137", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.1140.1140", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1141.1141", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1144.1144", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1140.1140", "start_pos": 1140, "end_pos": 1140, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GPLHSKVEKTFMNRLRKSTV", "down_seq": "SAPYLEELTQKVNKVEPYEQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1140" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41832-1.1137.1137", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.1138.1138", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.1141.1141", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1144.1144", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1141.1141", "start_pos": 1141, "end_pos": 1141, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLHSKVEKTFMNRLRKSTVS", "down_seq": "APYLEELTQKVNKVEPYEQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1141" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P41832-1.1137.1137", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1138.1138", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.1140.1140", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1144.1144", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1144.1144", "start_pos": 1144, "end_pos": 1144, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SKVEKTFMNRLRKSTVSSAP", "down_seq": "LEELTQKVNKVEPYEQNEDE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr1144" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P41832-1.1137.1137", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1138.1138", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.1140.1140", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1141.1141", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1273.1273", "start_pos": 1273, "end_pos": 1273, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LFGESLEKEKKSEDDTVKQE", "down_seq": "TGDSPAPPPPPPPPPPPPMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr1273" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P41832-1.1274.1274", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1277.1277", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1274.1274", "start_pos": 1274, "end_pos": 1274, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Regulation of the yeast formin Bni1p by the actin-regulating kinase Prk1p.", "journal": "Traffic (Copenhagen, Denmark)", "date": "2009-05", "authors": "Wang Junxia, Neo Suat Peng, Cai Mingjie", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FGESLEKEKKSEDDTVKQET", "down_seq": "GDSPAPPPPPPPPPPPPMAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811" } ], "site_lbl": "Thr1274" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P41832-1.1273.1273", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1277.1277", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1277.1277", "start_pos": 1277, "end_pos": 1277, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLEKEKKSEDDTVKQETTGD", "down_seq": "PAPPPPPPPPPPPPMALFGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser1277" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P41832-1.1273.1273", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1274.1274", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1302.1302", "start_pos": 1302, "end_pos": 1302, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PPPPPPPPPPMALFGKPKGE", "down_seq": "PPPPPLPSVLSSSTDGVIPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr1302" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1334.1334", "start_pos": 1334, "end_pos": 1334, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSTDGVIPPAPPMMPASQIK", "down_seq": "AVTSPLLPQSPSLFEKYPRP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1334" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P41832-1.1337.1337", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1338.1338", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.1344.1344", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.1346.1346", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1337.1337", "start_pos": 1337, "end_pos": 1337, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DGVIPPAPPMMPASQIKSAV", "down_seq": "SPLLPQSPSLFEKYPRPHKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr1337" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41832-1.1334.1334", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.1338.1338", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.1344.1344", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41832-1.1346.1346", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1338.1338", "start_pos": 1338, "end_pos": 1338, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVIPPAPPMMPASQIKSAVT", "down_seq": "PLLPQSPSLFEKYPRPHKKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1338" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P41832-1.1334.1334", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.1337.1337", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1344.1344", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.1346.1346", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1344.1344", "start_pos": 1344, "end_pos": 1344, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPMMPASQIKSAVTSPLLPQ", "down_seq": "PSLFEKYPRPHKKLKQLHWE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1344" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P41832-1.1334.1334", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P41832-1.1337.1337", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1338.1338", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.1346.1346", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1346.1346", "start_pos": 1346, "end_pos": 1346, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MMPASQIKSAVTSPLLPQSP", "down_seq": "LFEKYPRPHKKLKQLHWEKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ], "site_lbl": "Ser1346" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P41832-1.1334.1334", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P41832-1.1337.1337", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41832-1.1338.1338", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.1344.1344", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARSHSMQSKYSYSKRNSSQA", "down_seq": "NKLTRQHTGQSHSASSLLSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser135" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41832-1.117.117", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P41832-1.119.119", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P41832-1.122.122", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41832-1.154.154", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Regulation of the yeast formin Bni1p by the actin-regulating kinase Prk1p.", "journal": "Traffic (Copenhagen, Denmark)", "date": "2009-05", "authors": "Wang Junxia, Neo Suat Peng, Cai Mingjie", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KYSYSKRNSSQASNKLTRQH", "down_seq": "GQSHSASSLLSQGSLTNLSK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811" } ], "site_lbl": "Thr143" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41832-1.135.135", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.154.154", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.157.157", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASNKLTRQHTGQSHSASSLL", "down_seq": "QGSLTNLSKFTTPDGKIYLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser154" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41832-1.135.135", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P41832-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.157.157", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.166.166", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.157.157", "start_pos": 157, "end_pos": 157, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLTRQHTGQSHSASSLLSQG", "down_seq": "LTNLSKFTTPDGKIYLEMPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser157" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P41832-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.154.154", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41832-1.166.166", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLKNSGSKHSNSKE", "down_seq": "HSNSSSGIFQNLKRLANSNA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser15" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P41832-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P41832-1.20.20", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SHSASSLLSQGSLTNLSKFT", "down_seq": "PDGKIYLEMPSDPYEVEVLF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr166" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P41832-1.154.154", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P41832-1.157.157", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1781.1781", "start_pos": 1781, "end_pos": 1781, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKIVEEQQKRAQEKEKQKEN", "down_seq": "NSPSSEGNEEDEAEDRRAVM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1781" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P41832-1.1783.1783", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P41832-1.1786.1786", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1783.1783", "start_pos": 1783, "end_pos": 1783, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IVEEQQKRAQEKEKQKENSN", "down_seq": "PSSEGNEEDEAEDRRAVMDK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1783" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P41832-1.1781.1781", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.1786.1786", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1786.1786", "start_pos": 1786, "end_pos": 1786, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQQKRAQEKEKQKENSNSPS", "down_seq": "EGNEEDEAEDRRAVMDKLLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1786" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P41832-1.1781.1781", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.1783.1783", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLKNSGSKHSNSKESH", "down_seq": "NSSSGIFQNLKRLANSNATN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser17" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41832-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1816.1816", "start_pos": 1816, "end_pos": 1816, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DRRAVMDKLLEQLKNAGPAK", "down_seq": "DPSSARKRALVRKKYLSEKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1816" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P41832-1.1819.1819", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1820.1820", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1819.1819", "start_pos": 1819, "end_pos": 1819, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AVMDKLLEQLKNAGPAKSDP", "down_seq": "SARKRALVRKKYLSEKDNAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1819" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P41832-1.1816.1816", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.1820.1820", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1820.1820", "start_pos": 1820, "end_pos": 1820, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VMDKLLEQLKNAGPAKSDPS", "down_seq": "ARKRALVRKKYLSEKDNAPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1820" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P41832-1.1816.1816", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.1819.1819", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1855.1855", "start_pos": 1855, "end_pos": 1855, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDNAPQLLNDLDTEEGSILY", "down_seq": "PEAMDPTADTVIHAESPTPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1855" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P41832-1.1871.1871", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1871.1871", "start_pos": 1871, "end_pos": 1871, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SILYSPEAMDPTADTVIHAE", "down_seq": "PTPLATRGVMNTSEDLPSPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1871" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41832-1.1855.1855", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1877.1877", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41832-1.1889.1889", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41832-1.1891.1891", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1873.1873", "start_pos": 1873, "end_pos": 1873, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LYSPEAMDPTADTVIHAESP", "down_seq": "PLATRGVMNTSEDLPSPSKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Thr1873" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41832-1.1855.1855", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.1871.1871", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1877.1877", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.1889.1889", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41832-1.1891.1891", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41832-1.1893.1893", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1877.1877", "start_pos": 1877, "end_pos": 1877, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EAMDPTADTVIHAESPTPLA", "down_seq": "RGVMNTSEDLPSPSKTSALE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ], "site_lbl": "Thr1877" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P41832-1.1871.1871", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.1889.1889", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.1891.1891", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.1893.1893", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1883.1883", "start_pos": 1883, "end_pos": 1883, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ADTVIHAESPTPLATRGVMN", "down_seq": "SEDLPSPSKTSALEDQEEIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ], "site_lbl": "Thr1883" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P41832-1.1871.1871", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1877.1877", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1889.1889", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.1891.1891", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.1893.1893", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1889.1889", "start_pos": 1889, "end_pos": 1889, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Quantitative proteomics identifies unanticipated regulators of nitrogen- and glucose starvation.", "journal": "Molecular bioSystems", "date": "2014-08", "authors": "R\u00f8dk\u00e6r Steven V, Pultz Dennis, Brusch Michelle, Bennetzen Martin V, Falkenby Lasse G, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" } ] }, { "title": "Asc1p/RACK1 Connects Ribosomes to Eukaryotic Phosphosignaling.", "journal": "Molecular and cellular biology", "date": "2017-02-01", "authors": "Schmitt Kerstin, Smolinski Nadine, Neumann Piotr, Schmaul Samantha, Hofer-Pretz Verena, Braus Gerhard H, Valerius Oliver", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "27821475", "url": "https://glygen.org/publication/PubMed/27821475" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27821475", "url": "https://glygen.org/publication/PubMed/27821475", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AESPTPLATRGVMNTSEDLP", "down_seq": "PSKTSALEDQEEISDRARML", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "24909858", "url": "https://glygen.org/publication/PubMed/24909858" }, { "database": "PubMed", "id": "27821475", "url": "https://glygen.org/publication/PubMed/27821475" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1889" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41832-1.1871.1871", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P41832-1.1877.1877", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.1891.1891", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.1893.1893", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1891.1891", "start_pos": 1891, "end_pos": 1891, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPTPLATRGVMNTSEDLPSP", "down_seq": "KTSALEDQEEISDRARMLLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1891" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41832-1.1871.1871", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41832-1.1877.1877", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41832-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.1889.1889", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.1893.1893", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1893.1893", "start_pos": 1893, "end_pos": 1893, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TPLATRGVMNTSEDLPSPSK", "down_seq": "SALEDQEEISDRARMLLKEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" } ], "site_lbl": "Thr1893" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41832-1.1873.1873", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P41832-1.1877.1877", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.1883.1883", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.1889.1889", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.1891.1891", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1916.1916", "start_pos": 1916, "end_pos": 1916, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEDQEEISDRARMLLKELRG", "down_seq": "DTPVKQNSILDEHLEKLRAR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser1916" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P41832-1.1918.1918", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.1924.1924", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1918.1918", "start_pos": 1918, "end_pos": 1918, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DQEEISDRARMLLKELRGSD", "down_seq": "PVKQNSILDEHLEKLRARKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Thr1918" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P41832-1.1916.1916", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1924.1924", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1924.1924", "start_pos": 1924, "end_pos": 1924, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DRARMLLKELRGSDTPVKQN", "down_seq": "ILDEHLEKLRARKERSIGEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" } ], "site_lbl": "Ser1924" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41832-1.1916.1916", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.1918.1918", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.1940.1940", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1940.1940", "start_pos": 1940, "end_pos": 1940, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKQNSILDEHLEKLRARKER", "down_seq": "IGEASTGNRLSFK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1940" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41832-1.1924.1924", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.1946.1946", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P41832-1.1951.1951", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1946.1946", "start_pos": 1946, "end_pos": 1946, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Regulation of the yeast formin Bni1p by the actin-regulating kinase Prk1p.", "journal": "Traffic (Copenhagen, Denmark)", "date": "2009-05", "authors": "Wang Junxia, Neo Suat Peng, Cai Mingjie", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDEHLEKLRARKERSIGEAS", "down_seq": "GNRLSFK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19220811", "url": "https://glygen.org/publication/PubMed/19220811" } ], "site_lbl": "Thr1946" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P41832-1.1940.1940", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P41832-1.1951.1951", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.1951.1951", "start_pos": 1951, "end_pos": 1951, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EKLRARKERSIGEASTGNRL", "down_seq": "FK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1951" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41832-1.1940.1940", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P41832-1.1946.1946", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLKNSGSKHSNSKESHSN", "down_seq": "SSGIFQNLKRLANSNATNSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser19" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41832-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "", "down_seq": "SGIFQNLKRLANSNATNSNT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser20" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41832-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P41832-1.15.15", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41832-1.40.40", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDLQNELKKMRANTTSSSTA", "down_seq": "RTSMASDHHPILTANSSLSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser241" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P41832-1.244.244", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DHHPILTANSSLSSPKSVLM", "down_seq": "SASSPTSTVYSNSLNHSTTL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr268" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HHPILTANSSLSSPKSVLMT", "down_seq": "ASSPTSTVYSNSLNHSTTLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser269" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ILTANSSLSSPKSVLMTSAS", "down_seq": "PTSTVYSNSLNHSTTLSSVG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser272" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.275.275", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ANSSLSSPKSVLMTSASSPT", "down_seq": "TVYSNSLNHSTTLSSVGTST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser275" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41832-1.257.257", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P41832-1.258.258", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P41832-1.260.260", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P41832-1.261.261", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P41832-1.268.268", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.269.269", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.272.272", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVYSNSLNHSTTLSSVGTST", "down_seq": "KGKKLVSGSLKKQPSLNNIY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser296" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P41832-1.303.303", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41832-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NHSTTLSSVGTSTSKGKKLV", "down_seq": "GSLKKQPSLNNIYRGGAENN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser303" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P41832-1.296.296", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STTLSSVGTSTSKGKKLVSG", "down_seq": "LKKQPSLNNIYRGGAENNTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser305" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P41832-1.296.296", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.303.303", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41832-1.324.324", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P41832-1.325.325", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VGTSTSKGKKLVSGSLKKQP", "down_seq": "LNNIYRGGAENNTSASTLPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser311" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P41832-1.296.296", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41832-1.303.303", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P41832-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P41832-1.324.324", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.325.325", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.327.327", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.328.328", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.324.324", "start_pos": 324, "end_pos": 324, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GSLKKQPSLNNIYRGGAENN", "down_seq": "SASTLPGDRTNRPPIHYVQR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr324" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41832-1.305.305", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P41832-1.325.325", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P41832-1.327.327", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.328.328", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.328.328", "start_pos": 328, "end_pos": 328, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KQPSLNNIYRGGAENNTSAS", "down_seq": "LPGDRTNRPPIHYVQRILAD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr328" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P41832-1.311.311", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.324.324", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P41832-1.325.325", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P41832-1.327.327", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HSNSSSGIFQNLKRLANSNA", "down_seq": "NSNTGSPTYASQQQHSPVGN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr36" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41832-1.17.17", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P41832-1.19.19", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P41832-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P41832-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.44.44", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.52.52", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSGIFQNLKRLANSNATNSN", "down_seq": "GSPTYASQQQHSPVGNEVST", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr40" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P41832-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.44.44", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P41832-1.52.52", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GIFQNLKRLANSNATNSNTG", "down_seq": "PTYASQQQHSPVGNEVSTSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser42" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.44.44", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P41832-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P41832-1.61.61", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FQNLKRLANSNATNSNTGSP", "down_seq": "YASQQQHSPVGNEVSTSPAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Thr44" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P41832-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P41832-1.61.61", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSNATNSNTGSPTYASQQQH", "down_seq": "PVGNEVSTSPASSSSFRKLN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser52" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41832-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P41832-1.40.40", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P41832-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P41832-1.44.44", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P41832-1.61.61", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSPTYASQQQHSPVGNEVST", "down_seq": "PASSSSFRKLNAPSRSTSTE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser61" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P41832-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P41832-1.44.44", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P41832-1.52.52", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P41832-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P41832-1.77.77", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P41832-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.740.740", "start_pos": 740, "end_pos": 740, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AILESRALTKKLEEIQAERD", "down_seq": "LSEKLSKAEHGLVGQLEDEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser740" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNEVSTSPASSSSFRKLNAP", "down_seq": "RSTSTEARPLNKKSTLNTQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser75" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P41832-1.61.61", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.77.77", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P41832-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVSTSPASSSSFRKLNAPSR", "down_seq": "TSTEARPLNKKSTLNTQNLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ], "site_lbl": "Ser77" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P41832-1.61.61", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P41832-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSPASSSSFRKLNAPSRST", "down_seq": "TEARPLNKKSTLNTQNLSQY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser79" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P41832-1.61.61", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P41832-1.75.75", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P41832-1.77.77", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.829.829", "start_pos": 829, "end_pos": 829, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RPEESFNKNEGTRGMNSSLN", "down_seq": "SEKANIQKVLQDGLSRAKKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser829" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41832-1.944.944", "start_pos": 944, "end_pos": 944, "uniprot_canonical_ac": "P41832-1", "length": 1953, "uniprot_id": "BNI1_YEAST", "protein_name": "Protein BNI1", "refseq_ac": "NP_014128", "refseq_name": "formin BNI1", "gene_name": "BNI1", "gene_names_uniprotkb": "BNI1; N0646; PPF3; SHE5", "gene_names_refseq": "BNI1; PPF3; SHE5", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P41832", "url": "https://www.uniprot.org/uniprotkb/P41832" }, { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] } ], "crossref": [ { "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EADVNKLNDLRRALAEIQME", "down_seq": "NDISKFNVEERVNELFNEKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P41832", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P41832" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000005215", "url": "https://www.yeastgenome.org/locus/S000005215" } ], "site_lbl": "Ser944" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1082", "end_pos": "1082" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1089", "end_pos": "1089" }, { "start_pos": "1137", "end_pos": "1137" }, { "start_pos": "1138", "end_pos": "1138" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "1170", "end_pos": "1170" }, { "start_pos": "1175", "end_pos": "1175" }, { "start_pos": "1181", "end_pos": "1181" }, { "start_pos": "1273", "end_pos": "1273" }, { "start_pos": "1274", "end_pos": "1274" }, { "start_pos": "1277", "end_pos": "1277" }, { "start_pos": "1302", "end_pos": "1302" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1338", "end_pos": "1338" }, { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1346", "end_pos": "1346" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1781", "end_pos": "1781" }, { "start_pos": "1783", "end_pos": "1783" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "1816", "end_pos": "1816" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "1820", "end_pos": "1820" }, { "start_pos": "1855", "end_pos": "1855" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1877", "end_pos": "1877" }, { "start_pos": "1883", "end_pos": "1883" }, { "start_pos": "1889", "end_pos": "1889" }, { "start_pos": "1891", "end_pos": "1891" }, { "start_pos": "1893", "end_pos": "1893" }, { "start_pos": "1916", "end_pos": "1916" }, { "start_pos": "1918", "end_pos": "1918" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1940", "end_pos": "1940" }, { "start_pos": "1946", "end_pos": "1946" }, { "start_pos": "1951", "end_pos": "1951" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "740", "end_pos": "740" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "829", "end_pos": "829" }, { "start_pos": "944", "end_pos": "944" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "GLY_001160", "url": "https://data.glygen.org/GLY_001160", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TKLKPSPLLNNDDKNSSPSP", "down_seq": "ASTSSMKKLKSGLFNKNEAK", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr247", "evidence": [ { "id": "GLY_001160", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001160" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr247" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P42073-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42073-1.242.242", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42073-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42073-1.245.245", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" }, { "database": "O-GlcNAc Atlas", "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASTSSMKKLKSGLFNKNEAK", "down_seq": "TESLPTSSKKKLSFSKYLNK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser268", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P42073", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42073" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P42073-1.269.269", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42073-1.271.271", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42073-1.275.275", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42073-1.276.276", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" }, { "database": "O-GlcNAc Atlas", "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "STSSMKKLKSGLFNKNEAKS", "down_seq": "ESLPTSSKKKLSFSKYLNKD", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr269", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P42073", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42073" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P42073-1.268.268", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42073-1.271.271", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42073-1.275.275", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42073-1.276.276", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" }, { "database": "O-GlcNAc Atlas", "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSMKKLKSGLFNKNEAKSTE", "down_seq": "LPTSSKKKLSFSKYLNKDDA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser271", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P42073", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42073" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P42073-1.268.268", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42073-1.269.269", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42073-1.275.275", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42073-1.276.276", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" }, { "database": "O-GlcNAc Atlas", "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KLKSGLFNKNEAKSTESLPT", "down_seq": "SKKKLSFSKYLNKDDADMTK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser275", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P42073", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42073" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P42073-1.268.268", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42073-1.269.269", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42073-1.271.271", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42073-1.276.276", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" }, { "database": "O-GlcNAc Atlas", "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKSGLFNKNEAKSTESLPTS", "down_seq": "KKKLSFSKYLNKDDADMTKL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser276", "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P42073", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P42073" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P42073-1.268.268", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42073-1.269.269", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42073-1.271.271", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42073-1.275.275", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Identification of novel O-GlcNAc transferase substrates using yeast cells expressing OGT.", "journal": "The Journal of general and applied microbiology", "date": "2021-04-16", "authors": "Li Feng, Yang Ganglong, Tachikawa Hiroyuki, Shao Kankai, Yang Yan, Gao Xiao-Dong, Nakanishi Hideki", "evidence": [ { "database": "O-GlcNAc Database", "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" }, { "database": "O-GlcNAc Atlas", "id": "P42073", "url": "https://oglcnac.org/atlas/detail/P42073" } ], "reference": [ { "type": "PubMed", "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814" } ] } ], "crossref": [ { "id": "33229814", "url": "https://glygen.org/publication/PubMed/33229814", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42073", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33229814", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33229814" }, { "id": "P42073", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42073" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MYLDYLNQLIKLKHEKQHHS", "down_seq": "PPIANDVSLDFFVNQLPKFS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr106" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KEKEKEKDKSKVKMKTKLKP", "down_seq": "PLLNNDDKNSSPSPTASTSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser232" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P42073-1.242.242", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42073-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42073-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42073-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KVKMKTKLKPSPLLNNDDKN", "down_seq": "SPSPTASTSSMKKLKSGLFN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser242" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P42073-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42073-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42073-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42073-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKMKTKLKPSPLLNNDDKNS", "down_seq": "PSPTASTSSMKKLKSGLFNK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P42073-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42073-1.242.242", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42073-1.245.245", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42073-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MKTKLKPSPLLNNDDKNSSP", "down_seq": "PTASTSSMKKLKSGLFNKNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser245" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Ser245" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser245" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P42073-1.232.232", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42073-1.242.242", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42073-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42073-1.247.247", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.337.337", "start_pos": 337, "end_pos": 337, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNIISSSTSGSSTTTVATPA", "down_seq": "SEEPLKKKTKISVQDSNVQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser337" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ILRNGKPKKARISSIKFLDD", "down_seq": "QLIKVYGDDLPNQGLQVSPT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser378" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P42073-1.396.396", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42073-1.398.398", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "J. Proteome Res.", "date": "2007", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DDSQLIKVYGDDLPNQGLQV", "down_seq": "PTQLKKILKPFKEGEPKEII", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser396" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42073-1.378.378", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42073-1.398.398", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42073-1.398.398", "start_pos": 398, "end_pos": 398, "uniprot_canonical_ac": "P42073-1", "length": 533, "uniprot_id": "REF2_YEAST", "protein_name": "RNA end formation protein 2", "refseq_ac": "NP_010481", "refseq_name": "RNA-processing protein REF2", "gene_name": "REF2", "gene_names_uniprotkb": "REF2; YD9346.06", "gene_names_refseq": "REF2", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42073", "url": "https://www.uniprot.org/uniprotkb/P42073" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SQLIKVYGDDLPNQGLQVSP", "down_seq": "QLKKILKPFKEGEPKEIILF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000002603", "url": "https://www.yeastgenome.org/locus/S000002603" }, { "database": "iPTMnet", "id": "P42073", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42073" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Thr398" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "247", "end_pos": "247" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "398", "end_pos": "398" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42073-1.378.378", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42073-1.396.396", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42837-1.469.469", "start_pos": 469, "end_pos": 469, "uniprot_canonical_ac": "P42837-1", "length": 879, "uniprot_id": "FIG4_YEAST", "protein_name": "Polyphosphoinositide phosphatase", "refseq_ac": "NP_014074", "refseq_name": "phosphatidylinositol-3,5-bisphosphate 5-phosphatase", "gene_name": "FIG4", "gene_names_uniprotkb": "FIG4; N0330", "gene_names_refseq": "FIG4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The Vac14p-Fig4p complex acts independently of Vac7p and couples PI3,5P2 synthesis and turnover.", "journal": "The Journal of cell biology", "date": "2006-02-27", "authors": "Duex Jason E, Tang Fusheng, Weisman Lois S", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "reference": [ { "type": "PubMed", "id": "16492811", "url": "https://glygen.org/publication/PubMed/16492811" } ] } ], "crossref": [ { "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16492811", "url": "https://glygen.org/publication/PubMed/16492811", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NGPDFASTKIQEGICRSNCI", "down_seq": "CLDRTNAAQFVIGKRALGCQ", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "N", "comment": "Partially defective in both hyperosmotic shock-induced PtdIns(3,5)P2 elevation and turnover.", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" }, { "database": "PubMed", "id": "16492811", "url": "https://glygen.org/publication/PubMed/16492811" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "695", "end_pos": "695" }, { "start_pos": "717", "end_pos": "717" }, { "start_pos": "829", "end_pos": "829" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42837-1.519.519", "start_pos": 519, "end_pos": 519, "uniprot_canonical_ac": "P42837-1", "length": 879, "uniprot_id": "FIG4_YEAST", "protein_name": "Polyphosphoinositide phosphatase", "refseq_ac": "NP_014074", "refseq_name": "phosphatidylinositol-3,5-bisphosphate 5-phosphatase", "gene_name": "FIG4", "gene_names_uniprotkb": "FIG4; N0330", "gene_names_refseq": "FIG4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Regulation of Fab1 phosphatidylinositol 3-phosphate 5-kinase pathway by Vac7 protein and Fig4, a polyphosphoinositide phosphatase family member.", "journal": "Molecular biology of the cell", "date": "2002-04", "authors": "Gary Jonathan D, Sato Trey K, Stefan Christopher J, Bonangelino Cecilia J, Weisman Lois S, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "reference": [ { "type": "PubMed", "id": "11950935", "url": "https://glygen.org/publication/PubMed/11950935" } ] }, { "title": "Vacuole size control: regulation of PtdIns(3,5)P2 levels by the vacuole-associated Vac14-Fig4 complex, a PtdIns(3,5)P2-specific phosphatase.", "journal": "Molecular biology of the cell", "date": "2004-01", "authors": "Rudge Simon A, Anderson Deborah M, Emr Scott D", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "reference": [ { "type": "PubMed", "id": "14528018", "url": "https://glygen.org/publication/PubMed/14528018" } ] }, { "title": "The Vac14p-Fig4p complex acts independently of Vac7p and couples PI3,5P2 synthesis and turnover.", "journal": "The Journal of cell biology", "date": "2006-02-27", "authors": "Duex Jason E, Tang Fusheng, Weisman Lois S", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "reference": [ { "type": "PubMed", "id": "16492811", "url": "https://glygen.org/publication/PubMed/16492811" } ] } ], "crossref": [ { "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11950935", "url": "https://glygen.org/publication/PubMed/11950935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14528018", "url": "https://glygen.org/publication/PubMed/14528018", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16492811", "url": "https://glygen.org/publication/PubMed/16492811", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SYLEYDSDIVNILTELFHDL", "down_seq": "DTIALQYGGSHLVNTMETYR", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "R", "comment": "In FIG4-1; loss of catalytic activity in vitro. Almost 3-fold increase in PtdIns(3,5)P2 level in vivo. Partially defective in both hyperosmotic shock-induced PtdIns(3,5)P2 elevation and turnover.", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" }, { "database": "PubMed", "id": "11950935", "url": "https://glygen.org/publication/PubMed/11950935" }, { "database": "PubMed", "id": "14528018", "url": "https://glygen.org/publication/PubMed/14528018" }, { "database": "PubMed", "id": "16492811", "url": "https://glygen.org/publication/PubMed/16492811" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "695", "end_pos": "695" }, { "start_pos": "717", "end_pos": "717" }, { "start_pos": "829", "end_pos": "829" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42837-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "P42837-1", "length": 879, "uniprot_id": "FIG4_YEAST", "protein_name": "Polyphosphoinositide phosphatase", "refseq_ac": "NP_014074", "refseq_name": "phosphatidylinositol-3,5-bisphosphate 5-phosphatase", "gene_name": "FIG4", "gene_names_uniprotkb": "FIG4; N0330", "gene_names_refseq": "FIG4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mutation of FIG4 causes neurodegeneration in the pale tremor mouse and patients with CMT4J.", "journal": "Nature", "date": "2007", "authors": "Chow CY, Zhang Y, Dowling JJ, Jin N, Adamska M, Shiga K, Szigeti K, Shy ME, Li J, Zhang X, Lupski JR, Weisman LS, Meisler MH", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "reference": [ { "type": "PubMed", "id": "17572665", "url": "https://glygen.org/publication/PubMed/17572665" } ] } ], "crossref": [ { "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17572665", "url": "https://glygen.org/publication/PubMed/17572665", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KDRMYIVGSNKRETMFRILE", "down_seq": "DLTVPRGELTVLEDNVFFTR", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "T", "comment": "Defective activation of FAB1.", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" }, { "database": "PubMed", "id": "17572665", "url": "https://glygen.org/publication/PubMed/17572665" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "695", "end_pos": "695" }, { "start_pos": "717", "end_pos": "717" }, { "start_pos": "829", "end_pos": "829" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42837-1.695.695", "start_pos": 695, "end_pos": 695, "uniprot_canonical_ac": "P42837-1", "length": 879, "uniprot_id": "FIG4_YEAST", "protein_name": "Polyphosphoinositide phosphatase", "refseq_ac": "NP_014074", "refseq_name": "phosphatidylinositol-3,5-bisphosphate 5-phosphatase", "gene_name": "FIG4", "gene_names_uniprotkb": "FIG4; N0330", "gene_names_refseq": "FIG4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005269", "url": "https://www.yeastgenome.org/locus/S000005269", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YNMNSTRRYHNALSKQDKAM", "down_seq": "PFTSRKQSWLNNKLKMITSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005269", "url": "https://www.yeastgenome.org/locus/S000005269" }, { "database": "iPTMnet", "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser695" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "695", "end_pos": "695" }, { "start_pos": "717", "end_pos": "717" }, { "start_pos": "829", "end_pos": "829" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42837-1.717.717", "start_pos": 717, "end_pos": 717, "uniprot_canonical_ac": "P42837-1", "length": 879, "uniprot_id": "FIG4_YEAST", "protein_name": "Polyphosphoinositide phosphatase", "refseq_ac": "NP_014074", "refseq_name": "phosphatidylinositol-3,5-bisphosphate 5-phosphatase", "gene_name": "FIG4", "gene_names_uniprotkb": "FIG4; N0330", "gene_names_refseq": "FIG4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000005269", "url": "https://www.yeastgenome.org/locus/S000005269", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FTSRKQSWLNNKLKMITSSK", "down_seq": "LEKAEGRVVETTDLDRDTSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000005269", "url": "https://www.yeastgenome.org/locus/S000005269" }, { "database": "iPTMnet", "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser717" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "695", "end_pos": "695" }, { "start_pos": "717", "end_pos": "717" }, { "start_pos": "829", "end_pos": "829" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42837-1.829.829", "start_pos": 829, "end_pos": 829, "uniprot_canonical_ac": "P42837-1", "length": 879, "uniprot_id": "FIG4_YEAST", "protein_name": "Polyphosphoinositide phosphatase", "refseq_ac": "NP_014074", "refseq_name": "phosphatidylinositol-3,5-bisphosphate 5-phosphatase", "gene_name": "FIG4", "gene_names_uniprotkb": "FIG4; N0330", "gene_names_refseq": "FIG4", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" }, { "database": "iPTMnet", "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] } ], "crossref": [ { "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "S000005269", "url": "https://www.yeastgenome.org/locus/S000005269", "database": "SGD", "categories": [ "Organism-specific" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDDENDEMTTEALLIAPDHV", "down_seq": "VDEKFYEKVLNVDDYKPALD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42837", "url": "https://www.uniprot.org/uniprotkb/P42837" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P42837", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42837" }, { "database": "SGD", "id": "S000005269", "url": "https://www.yeastgenome.org/locus/S000005269" } ], "site_lbl": "Ser829" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "469", "end_pos": "469" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "695", "end_pos": "695" }, { "start_pos": "717", "end_pos": "717" }, { "start_pos": "829", "end_pos": "829" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7KY8", "url": "https://www.rcsb.org/structure/7KY8", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KYA", "url": "https://www.rcsb.org/structure/7KYA", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KYB", "url": "https://www.rcsb.org/structure/7KYB", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KYC", "url": "https://www.rcsb.org/structure/7KYC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY5", "url": "https://www.rcsb.org/structure/7KY5", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY8|B|113", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KYA|B|113", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KYB|B|113", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KYC|B|113", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY5|B|113", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ILAQNSKVDEVTIYYQDCMT", "down_seq": "ATSSWSDIPSEHWQFVFHKY", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7KY8&bu=0&command=select+.B:113;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn113", "evidence": [ { "id": "P42838", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "id": "7KY8", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY8" }, { "id": "7KYA", "database": "PDB", "url": "https://www.rcsb.org/structure/7KYA" }, { "id": "7KYB", "database": "PDB", "url": "https://www.rcsb.org/structure/7KYB" }, { "id": "7KYC", "database": "PDB", "url": "https://www.rcsb.org/structure/7KYC" }, { "id": "7KY5", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY5" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P42838-1.110.110", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42838-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Transport mechanism of P4 ATPase phosphatidylcholine flippases.", "journal": "eLife", "date": "2020-12-15", "authors": "Bai Lin, You Qinglong, Jain Bhawik K, Duan H Diessel, Kovach Amanda, Graham Todd R, Li Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7KY8", "url": "https://www.rcsb.org/structure/7KY8", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY9", "url": "https://www.rcsb.org/structure/7KY9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY8|B|240", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY9|B|240", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SKNADGKIYYPCGLIANSMF", "down_seq": "DTFPLQLTNVGDTSNNYSLT", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7KY8&bu=0&command=select+.B:240;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn240", "evidence": [ { "id": "P42838", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "id": "33320091", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33320091" }, { "id": "7KY8", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY8" }, { "id": "7KY9", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P42838-1.231.231", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42838-1.237.237", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42838-1.256.256", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Transport mechanism of P4 ATPase phosphatidylcholine flippases.", "journal": "eLife", "date": "2020-12-15", "authors": "Bai Lin, You Qinglong, Jain Bhawik K, Duan H Diessel, Kovach Amanda, Graham Todd R, Li Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7KY5", "url": "https://www.rcsb.org/structure/7KY5", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY8", "url": "https://www.rcsb.org/structure/7KY8", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY9", "url": "https://www.rcsb.org/structure/7KY9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY8|B|256", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY9|B|256", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY5|B|256", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NSMFNDTFPLQLTNVGDTSN", "down_seq": "YSLTNKGINWESDKKRYKKT", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7KY8&bu=0&command=select+.B:256;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn256", "evidence": [ { "id": "P42838", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "id": "33320091", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33320091" }, { "id": "7KY5", "database": "PDB", "url": "https://www.rcsb.org/sequence/7KY5" }, { "id": "7KY8", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY8" }, { "id": "7KY9", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42838-1.237.237", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42838-1.240.240", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.279.279", "start_pos": 279, "end_pos": 279, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LTNKGINWESDKKRYKKTKY", "down_seq": "YTQIAPPPYWEKMYPDGYNE", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn279", "evidence": [ { "id": "P42838", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P42838-1.298.298", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42838-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Transport mechanism of P4 ATPase phosphatidylcholine flippases.", "journal": "eLife", "date": "2020-12-15", "authors": "Bai Lin, You Qinglong, Jain Bhawik K, Duan H Diessel, Kovach Amanda, Graham Todd R, Li Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7KY8", "url": "https://www.rcsb.org/structure/7KY8", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY9", "url": "https://www.rcsb.org/structure/7KY9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KYB", "url": "https://www.rcsb.org/structure/7KYB", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KYC", "url": "https://www.rcsb.org/structure/7KYC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY8|B|298", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY9|B|298", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KYB|B|298", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KYC|B|298", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YNYTQIAPPPYWEKMYPDGY", "down_seq": "ETNIPDIQDWEEFQNWMRPG", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7KY8&bu=0&command=select+.B:298;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn298", "evidence": [ { "id": "P42838", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "id": "33320091", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33320091" }, { "id": "7KY8", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY8" }, { "id": "7KY9", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY9" }, { "id": "7KYB", "database": "PDB", "url": "https://www.rcsb.org/structure/7KYB" }, { "id": "7KYC", "database": "PDB", "url": "https://www.rcsb.org/structure/7KYC" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42838-1.279.279", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Transport mechanism of P4 ATPase phosphatidylcholine flippases.", "journal": "eLife", "date": "2020-12-15", "authors": "Bai Lin, You Qinglong, Jain Bhawik K, Duan H Diessel, Kovach Amanda, Graham Todd R, Li Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7KY8", "url": "https://www.rcsb.org/structure/7KY8", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY9", "url": "https://www.rcsb.org/structure/7KY9", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY5", "url": "https://www.rcsb.org/structure/7KY5", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "7KY8|B|332", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY9|B|332", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "7KY5|B|332", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QNWMRPGAFDKITKLIRINK", "down_seq": "DTLPAGEYQLDIGLHWPVLE", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=7KY8&bu=0&command=select+.B:332;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn332", "evidence": [ { "id": "P42838", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "id": "33320091", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33320091" }, { "id": "7KY8", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY8" }, { "id": "7KY9", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY9" }, { "id": "7KY5", "database": "PDB", "url": "https://www.rcsb.org/structure/7KY5" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "GGCILAQNSKVDEVTIYYQD", "down_seq": "MTNATSSWSDIPSEHWQFVF", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Strongly reduces interaction with DNF1. Mildly resistant to miltefosine. Decreases protein level. Normal protein level; when associated with C-159.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P42838-1.113.113", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "APQWRFVDDESDDFTKQRGT", "down_seq": "QIRFTTPSDMKNNVYLNYVL", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Strongly reduces interaction with DNF1. Mildly resistant to miltefosine. Decreases protein level. Normal protein level; when associated with C-110.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "DQIRGEDASYETVHDATGIN", "down_seq": "KPLSKNADGKIYYPCGLIAN", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Decreases DNF1 activity. Reduces interaction with DNF1. Resistant to miltefosine. Sensitive to duramycin.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P42838-1.231.231", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "ATGINCKPLSKNADGKIYYP", "down_seq": "GLIANSMFNDTFPLQLTNVG", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Mildly decreases DNF1 activity. Reduces interaction with DNF1. Resistant to miltefosine.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P42838-1.216.216", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42838-1.237.237", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42838-1.240.240", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPLSKNADGKIYYPCGLIAN", "down_seq": "MFNDTFPLQLTNVGDTSNNY", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "L", "comment": "Strongly reduces interaction with DNF1.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P42838-1.231.231", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42838-1.240.240", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42838-1.256.256", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GKKGIYLTHGSHLGGRNPFL", "down_seq": "IVYLIGGCICAAMALILLTF", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "E", "comment": "Reduces interaction with DNF1.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ICAAMALILLTFWLFGGRKI", "down_seq": "DASSLSWNMK", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "V", "comment": "Strongly reduces interaction with DNF1.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Transport mechanism of P4 ATPase phosphatidylcholine flippases.", "journal": "eLife", "date": "2020-12-15", "authors": "Bai Lin, You Qinglong, Jain Bhawik K, Duan H Diessel, Kovach Amanda, Graham Todd R, Li Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838#ptm_processing" }, { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EDVDASEFEEDEVKPVRTKN", "down_seq": "RPKEDAFTQQRLAAINPVLT", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Increases glucosylceramide transport activity of DNF1 and DNF2, but not their phosphatidylethanolamine or phosphatidylcholine transport activity.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "33320091", "url": "https://glygen.org/publication/PubMed/33320091" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P42838-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42838-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42838-1.65.65", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PVRTKNRRPKEDAFTQQRLA", "down_seq": "INPVLTPRTVLPLYLLIAVV", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "V", "comment": "Mildly reduces interaction with DNF1.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P42838-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42838-1.51.51", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42838-1.83.83", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Mapping functional interactions in a heterodimeric phospholipid pump.", "journal": "The Journal of biological chemistry", "date": "2012-08-31", "authors": "Puts Catheleyne F, Panatala Radhakrishnan, Hennrich Hanka, Tsareva Alina, Williamson Patrick, Holthuis Joost C M", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "reference": [ { "type": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LAAINPVLTPRTVLPLYLLI", "down_seq": "VVFVIVGGCILAQNSKVDEV", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "T", "comment": "Reduces interaction with DNF1.", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "22791719", "url": "https://glygen.org/publication/PubMed/22791719" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42838-1.65.65", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005267", "url": "https://www.yeastgenome.org/locus/S000005267", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NFDLGQVGEVFRRKDKGAIV", "down_seq": "GDNPEEEEDVDASEFEEDEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000005267", "url": "https://www.yeastgenome.org/locus/S000005267" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser23" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P42838-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000005267", "url": "https://www.yeastgenome.org/locus/S000005267", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDKGAIVSGDNPEEEEDVDA", "down_seq": "EFEEDEVKPVRTKNRRPKED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000005267", "url": "https://www.yeastgenome.org/locus/S000005267" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser36" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P42838-1.23.23", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42838-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42838-1.51.51", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42838-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P42838-1", "length": 414, "uniprot_id": "LEM3_YEAST", "protein_name": "Phospholipid-transporting ATPase accessory subunit LEM3", "refseq_ac": "NP_014076", "refseq_name": "Lem3p", "gene_name": "LEM3", "gene_names_uniprotkb": "LEM3; BRE3; N0333; ROS3", "gene_names_refseq": "BRE3; LEM3; ROS3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42838", "url": "https://www.uniprot.org/uniprotkb/P42838" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EEEEDVDASEFEEDEVKPVR", "down_seq": "KNRRPKEDAFTQQRLAAINP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42838", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42838" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Thr48" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "332", "end_pos": "332" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "23", "end_pos": "23" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "48", "end_pos": "48" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42838-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42838-1.51.51", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42838-1.65.65", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42949-1.88.90", "start_pos": 88, "end_pos": 90, "uniprot_canonical_ac": "P42949-1", "length": 149, "uniprot_id": "TIM16_YEAST", "protein_name": "Mitochondrial import inner membrane translocase subunit TIM16", "refseq_ac": "NP_012431", "refseq_name": "import motor complex subunit PAM16", "gene_name": "PAM16", "gene_names_uniprotkb": "PAM16; J0822; TIM16", "gene_names_refseq": "MIA1; PAM16; TIM16", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "The presequence translocase-associated protein import motor of mitochondria. Pam16 functions in an antagonistic manner to Pam18.", "journal": "The Journal of biological chemistry", "date": "2004-09-03", "authors": "Li Yanfeng, Dudek Jan, Guiard Bernard, Pfanner Nikolaus, Rehling Peter, Voos Wolfgang", "evidence": [ { "database": "UniProtKB", "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949" } ], "reference": [ { "type": "PubMed", "id": "15218029", "url": "https://glygen.org/publication/PubMed/15218029" } ] } ], "crossref": [ { "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15218029", "url": "https://glygen.org/publication/PubMed/15218029", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DKE", "start_aa": "D", "up_seq": "KGDLNMDKINNRFNYLFEVN", "down_seq": "KGGSFYLQSKVYRAAERLKW", "mutagenesis": [ { "sequence_org": "DKE", "sequence_mut": "HPD", "comment": "Does not confer ability to stimulate the ATPase activity of mtHSP70.", "evidence": [ { "database": "UniProtKB", "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949" }, { "database": "PubMed", "id": "15218029", "url": "https://glygen.org/publication/PubMed/15218029" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "88", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "67", "end_pos": "67" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42949-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "P42949-1", "length": 149, "uniprot_id": "TIM16_YEAST", "protein_name": "Mitochondrial import inner membrane translocase subunit TIM16", "refseq_ac": "NP_012431", "refseq_name": "import motor complex subunit PAM16", "gene_name": "PAM16", "gene_names_uniprotkb": "PAM16; J0822; TIM16", "gene_names_refseq": "MIA1; PAM16; TIM16", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000003640", "url": "https://www.yeastgenome.org/locus/S000003640", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STAKPPPNSTNSSGADNSAS", "down_seq": "NQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003640", "url": "https://www.yeastgenome.org/locus/S000003640" }, { "database": "iPTMnet", "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser147" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "88", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "67", "end_pos": "67" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42949-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P42949-1", "length": 149, "uniprot_id": "TIM16_YEAST", "protein_name": "Mitochondrial import inner membrane translocase subunit TIM16", "refseq_ac": "NP_012431", "refseq_name": "import motor complex subunit PAM16", "gene_name": "PAM16", "gene_names_uniprotkb": "PAM16; J0822; TIM16", "gene_names_refseq": "MIA1; PAM16; TIM16", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003640", "url": "https://www.yeastgenome.org/locus/S000003640", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YRQAASQSVKQGATNASRRG", "down_seq": "GKGEYGGITLDESCKILNIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003640", "url": "https://www.yeastgenome.org/locus/S000003640" }, { "database": "iPTMnet", "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr45" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "88", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "67", "end_pos": "67" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P42949-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P42949-1", "length": 149, "uniprot_id": "TIM16_YEAST", "protein_name": "Mitochondrial import inner membrane translocase subunit TIM16", "refseq_ac": "NP_012431", "refseq_name": "import motor complex subunit PAM16", "gene_name": "PAM16", "gene_names_uniprotkb": "PAM16; J0822; TIM16", "gene_names_refseq": "MIA1; PAM16; TIM16", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P42949", "url": "https://www.uniprot.org/uniprotkb/P42949" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000003640", "url": "https://www.yeastgenome.org/locus/S000003640", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KGEYGGITLDESCKILNIEE", "down_seq": "KGDLNMDKINNRFNYLFEVN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000003640", "url": "https://www.yeastgenome.org/locus/S000003640" }, { "database": "iPTMnet", "id": "P42949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42949" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser67" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "88", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "147", "end_pos": "147" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "67", "end_pos": "67" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKLELTGDTSKRLLDINVLK", "down_seq": "HNSKSDINVSLSMLGVNGDI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser106" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P43535-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43535-1.94.94", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43535-1.95.95", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43535-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43535-1.111.111", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELTGDTSKRLLDINVLKSHN", "down_seq": "KSDINVSLSMLGVNGDIEHT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser109" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43535-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43535-1.94.94", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43535-1.95.95", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43535-1.106.106", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43535-1.111.111", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TGDTSKRLLDINVLKSHNSK", "down_seq": "DINVSLSMLGVNGDIEHTGR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser111" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43535-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43535-1.94.94", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43535-1.95.95", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43535-1.106.106", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43535-1.109.109", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKINERLKEMDVLRQEFEED", "down_seq": "LEVKKLDNEREDLDNHLIQI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser311" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EREDLDNHLIQISDKLVDME", "down_seq": "DKAEARAASILYGLGFSTEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser340" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MA", "down_seq": "IGSQVRKAASSIDPIVTDYA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser3" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P43535-1.6.6", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MASIG", "down_seq": "QVRKAASSIDPIVTDYAVGY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P43535-1.3.3", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.742.742", "start_pos": 742, "end_pos": 742, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGTVKRFEGTIYDYRDYILQ", "down_seq": "ADAAGVVKKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser742" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ESILKQLTTQLKENEAKLEL", "down_seq": "GDTSKRLLDINVLKSHNSKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr91" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P43535-1.94.94", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43535-1.95.95", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43535-1.106.106", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43535-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43535-1.111.111", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control.", "journal": "Molecular cell", "date": "2021-05-06", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Pillet Benjamin, Hu Zehan, Garcia Osuna Guillermo Miguel, Kressler Dieter, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33743194", "url": "https://glygen.org/publication/PubMed/33743194" } ] }, { "title": "Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast.", "journal": "Cell reports", "date": "2021-12-28", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Hu Zehan, Jaquenoud Malika, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33743194", "url": "https://glygen.org/publication/PubMed/33743194", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKQLTTQLKENEAKLELTGD", "down_seq": "SKRLLDINVLKSHNSKSDIN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "33743194", "url": "https://glygen.org/publication/PubMed/33743194" }, { "database": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ], "site_lbl": "Thr94" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P43535-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43535-1.95.95", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43535-1.106.106", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43535-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43535-1.111.111", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43535-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "P43535-1", "length": 752, "uniprot_id": "GCN20_YEAST", "protein_name": "Protein GCN20", "refseq_ac": "NP_116664", "refseq_name": "putative AAA family ATPase GCN20", "gene_name": "GCN20", "gene_names_uniprotkb": "GCN20", "gene_names_refseq": "GCN20", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43535", "url": "https://www.uniprot.org/uniprotkb/P43535" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control.", "journal": "Molecular cell", "date": "2021-05-06", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Pillet Benjamin, Hu Zehan, Garcia Osuna Guillermo Miguel, Kressler Dieter, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "33743194", "url": "https://glygen.org/publication/PubMed/33743194" } ] }, { "title": "Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast.", "journal": "Cell reports", "date": "2021-12-28", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Hu Zehan, Jaquenoud Malika, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" } ], "reference": [ { "type": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ] } ], "crossref": [ { "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33743194", "url": "https://glygen.org/publication/PubMed/33743194", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KQLTTQLKENEAKLELTGDT", "down_seq": "KRLLDINVLKSHNSKSDINV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001905", "url": "https://www.yeastgenome.org/locus/S000001905" }, { "database": "iPTMnet", "id": "P43535", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43535" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "33743194", "url": "https://glygen.org/publication/PubMed/33743194" }, { "database": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ], "site_lbl": "Ser95" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P43535-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43535-1.94.94", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43535-1.106.106", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43535-1.109.109", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43535-1.111.111", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1663.1664", "start_pos": 1663, "end_pos": 1664, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Acetylation-mediated proteasomal degradation of core histones during DNA repair and spermatogenesis.", "journal": "Cell", "date": "2013", "authors": "Qian MX, Pang Y, Liu CH, Haratake K, Du BY, Ji DY, Wang GF, Zhu QQ, Song W, Yu Y, Zhang XX, Huang HT, Miao S, Chen LB, Zhang ZH, Liang YN, Liu S, Cha H, Yang D, Zhai Y, Komatsu T, Tsuruta F, Li H, Cao C, Li W, Li GH, Cheng Y, Chiba T, Wang L, Goldberg AL, Shen Y, Qiu XB", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "23706739", "url": "https://glygen.org/publication/PubMed/23706739" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23706739", "url": "https://glygen.org/publication/PubMed/23706739", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "YN", "start_aa": "Y", "up_seq": "ISSGFCELNMSDLFELCESY", "down_seq": "KDDKASMIMSVEIVAGLVCG", "mutagenesis": [ { "sequence_org": "YN", "sequence_mut": "HD", "comment": "Abolishes binding to acetylated histones.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "23706739", "url": "https://glygen.org/publication/PubMed/23706739" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.2139.2139", "start_pos": 2139, "end_pos": 2139, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism.", "journal": "The Journal of biological chemistry", "date": "2011-12-16", "authors": "Dange Thomas, Smith David, Noy Tahel, Rommel Philipp C, Jurzitza Lukas, Cordero Radames J B, Legendre Anne, Finley Daniel, Goldberg Alfred L, Schmidt Marion", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KFDRASFNTEELEDLEGVLW", "down_seq": "SYYA", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "D", "comment": "Does not affect binding to the proteasome.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P43583-1.2140.2140", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.2141.2141", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.2141.2143", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43583-1.2142.2142", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43583-1.2143.2143", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.2140.2140", "start_pos": 2140, "end_pos": 2140, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism.", "journal": "The Journal of biological chemistry", "date": "2011-12-16", "authors": "Dange Thomas, Smith David, Noy Tahel, Rommel Philipp C, Jurzitza Lukas, Cordero Radames J B, Legendre Anne, Finley Daniel, Goldberg Alfred L, Schmidt Marion", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FDRASFNTEELEDLEGVLWR", "down_seq": "YYA", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "H", "comment": "Abolishes binding to the proteasome.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P43583-1.2139.2139", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.2141.2141", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.2141.2143", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.2142.2142", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43583-1.2143.2143", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.2141.2141", "start_pos": 2141, "end_pos": 2141, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism.", "journal": "The Journal of biological chemistry", "date": "2011-12-16", "authors": "Dange Thomas, Smith David, Noy Tahel, Rommel Philipp C, Jurzitza Lukas, Cordero Radames J B, Legendre Anne, Finley Daniel, Goldberg Alfred L, Schmidt Marion", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DRASFNTEELEDLEGVLWRS", "down_seq": "YA", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "M", "comment": "Does not affect viability in the presence of cycloheximide.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43583-1.2139.2139", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.2140.2140", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "P43583-1.2141.2143", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.2142.2142", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.2143.2143", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.2141.2143", "start_pos": 2141, "end_pos": 2143, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening.", "journal": "Molecular cell", "date": "2010-03-12", "authors": "Sadre-Bazzaz Kianoush, Whitby Frank G, Robinson Howard, Formosa Tim, Hill Christopher P", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "20227375", "url": "https://glygen.org/publication/PubMed/20227375" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20227375", "url": "https://glygen.org/publication/PubMed/20227375", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "YYA", "start_aa": "Y", "up_seq": "DRASFNTEELEDLEGVLWRS", "down_seq": "", "mutagenesis": [ { "sequence_org": "YYA", "sequence_mut": "", "comment": "Loss of function.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "20227375", "url": "https://glygen.org/publication/PubMed/20227375" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43583-1.2139.2139", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.2140.2140", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "P43583-1.2141.2141", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.2142.2142", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "upstream", "id": "P43583-1.2143.2143", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.2142.2142", "start_pos": 2142, "end_pos": 2142, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism.", "journal": "The Journal of biological chemistry", "date": "2011-12-16", "authors": "Dange Thomas, Smith David, Noy Tahel, Rommel Philipp C, Jurzitza Lukas, Cordero Radames J B, Legendre Anne, Finley Daniel, Goldberg Alfred L, Schmidt Marion", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RASFNTEELEDLEGVLWRSY", "down_seq": "", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Loss of function; abolishes binding to the proteasome.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] }, { "sequence_org": "Y", "sequence_mut": "V", "comment": "Abolishes binding to the proteasome.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] }, { "sequence_org": "Y", "sequence_mut": "V", "comment": "Loss of function; abolishes binding to the proteasome.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P43583-1.2139.2139", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43583-1.2140.2140", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.2141.2141", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.2141.2143", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.2143.2143", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.2143.2143", "start_pos": 2143, "end_pos": 2143, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism.", "journal": "The Journal of biological chemistry", "date": "2011-12-16", "authors": "Dange Thomas, Smith David, Noy Tahel, Rommel Philipp C, Jurzitza Lukas, Cordero Radames J B, Legendre Anne, Finley Daniel, Goldberg Alfred L, Schmidt Marion", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "reference": [ { "type": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ASFNTEELEDLEGVLWRSYY", "down_seq": "", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "S", "comment": "Does not affect viability in the presence of cycloheximide.", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "22025621", "url": "https://glygen.org/publication/PubMed/22025621" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P43583-1.2139.2139", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43583-1.2140.2140", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43583-1.2141.2141", "categories": [ "mutagenesis_flag" ] }, { "distance": 0, "direction": "downstream", "id": "P43583-1.2141.2143", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.2142.2142", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1006.1006", "start_pos": 1006, "end_pos": 1006, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLSEYCINNVEELMKAPRHD", "down_seq": "EYGDMIQKYVLVMTHTLSGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1006" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1039.1039", "start_pos": 1039, "end_pos": 1039, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MTHTLSGSSLLFDPDFNKYR", "down_seq": "QSNLSYREKLILLKNIRENN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr1039" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P43583-1.1041.1041", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1041.1041", "start_pos": 1041, "end_pos": 1041, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HTLSGSSLLFDPDFNKYRTQ", "down_seq": "NLSYREKLILLKNIRENNCD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1041" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43583-1.1039.1039", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1074.1074", "start_pos": 1074, "end_pos": 1074, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NIRENNCDPQELDIDIEQIR", "down_seq": "GKDDEDYIESKDIEAGLNAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser1074" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SDRAQHMKNIYDPSSRWFSR", "down_seq": "VRPEFPIEEFLPYKTESHED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser115" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MTANNDDDIK", "down_seq": "PIPITNKTLSQLKRFERSPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser11" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P43583-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1355.1355", "start_pos": 1355, "end_pos": 1355, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MKIQVILNVLLIKKIHRKLM", "down_seq": "DYKDIGRLIFLLIECCRVNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Thr1355" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P43583-1.1357.1357", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1357.1357", "start_pos": 1357, "end_pos": 1357, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] } ], "crossref": [ { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IQVILNVLLIKKIHRKLMTD", "down_seq": "KDIGRLIFLLIECCRVNELE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ], "site_lbl": "Tyr1357" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43583-1.1355.1355", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.1486.1486", "start_pos": 1486, "end_pos": 1486, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RFVTQIQSNLESKPDKRAVF", "down_seq": "IISQISTKHPEIIHLVVKSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ], "site_lbl": "Ser1486" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MTANNDDDIKSPIPITNKTL", "down_seq": "QLKRFERSPGRPSSSQGEIK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser21" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P43583-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43583-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43583-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IKSPIPITNKTLSQLKRFER", "down_seq": "PGRPSSSQGEIKRKKSRLYA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00546-1", "kinase_gene_name": "CDC28", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser29" }, { "kinase_uniprot_canonical_ac": "P24869-1", "kinase_gene_name": "CLB2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Ser29" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser29" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43583-1.11.11", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43583-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43583-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43583-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PITNKTLSQLKRFERSPGRP", "down_seq": "SSQGEIKRKKSRLYAADGRP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser34" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P43583-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast.", "journal": "Cell reports", "date": "2021-12-28", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Hu Zehan, Jaquenoud Malika, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ] } ], "crossref": [ { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ITNKTLSQLKRFERSPGRPS", "down_seq": "SQGEIKRKKSRLYAADGRPH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ], "site_lbl": "Ser35" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P43583-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] }, { "title": "Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast.", "journal": "Cell reports", "date": "2021-12-28", "authors": "Dokl\u00e1dal Ladislav, Stumpe Michael, Hu Zehan, Jaquenoud Malika, Dengjel J\u00f6rn, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNKTLSQLKRFERSPGRPSS", "down_seq": "QGEIKRKKSRLYAADGRPHS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" }, { "database": "PubMed", "id": "34965436", "url": "https://glygen.org/publication/PubMed/34965436" } ], "site_lbl": "Ser36" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P43583-1.21.21", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43583-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43583-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43583-1.56.56", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RFERSPGRPSSSQGEIKRKK", "down_seq": "RLYAADGRPHSPLRARSATP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser45" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43583-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43583-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43583-1.56.56", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RSPGRPSSSQGEIKRKKSRL", "down_seq": "AADGRPHSPLRARSATPTLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Tyr48" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43583-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43583-1.34.34", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43583-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43583-1.56.56", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43583-1.66.66", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQGEIKRKKSRLYAADGRPH", "down_seq": "PLRARSATPTLQDQKLFNGM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser56" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43583-1.36.36", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43583-1.66.66", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.", "journal": "Nature biotechnology", "date": "2002-03", "authors": "Ficarro Scott B, McCleland Mark L, Stukenberg P Todd, Burke Daniel J, Ross Mark M, Shabanowitz Jeffrey, Hunt Donald F, White Forest M", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A.", "journal": "Cell reports", "date": "2013-01-31", "authors": "Bontron S\u00e9verine, Jaquenoud Malika, Vaga Stefania, Talarek Nicolas, Bodenmiller Bernd, Aebersold Ruedi, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23273919", "url": "https://glygen.org/publication/PubMed/23273919" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23273919", "url": "https://glygen.org/publication/PubMed/23273919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKKSRLYAADGRPHSPLRAR", "down_seq": "ATPTLQDQKLFNGMDSTSLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23273919", "url": "https://glygen.org/publication/PubMed/23273919" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser62" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43583-1.56.56", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43583-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43583-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43583-1.80.80", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-02-13", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae.", "journal": "Nature biotechnology", "date": "2002-03", "authors": "Ficarro Scott B, McCleland Mark L, Stukenberg P Todd, Burke Daniel J, Ross Mark M, Shabanowitz Jeffrey, Hunt Donald F, White Forest M", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.", "journal": "Genes & development", "date": "2009-08-15", "authors": "Huber Alexandre, Bodenmiller Bernd, Uotila Aino, Stahl Michael, Wanka Stefanie, Gerrits Bertran, Aebersold Ruedi, Loewith Robbie", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A.", "journal": "Cell reports", "date": "2013-01-31", "authors": "Bontron S\u00e9verine, Jaquenoud Malika, Vaga Stefania, Talarek Nicolas, Bodenmiller Bernd, Aebersold Ruedi, De Virgilio Claudio", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23273919", "url": "https://glygen.org/publication/PubMed/23273919" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23273919", "url": "https://glygen.org/publication/PubMed/23273919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSRLYAADGRPHSPLRARSA", "down_seq": "PTLQDQKLFNGMDSTSLLNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "11875433", "url": "https://glygen.org/publication/PubMed/11875433" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19684113", "url": "https://glygen.org/publication/PubMed/19684113" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "23273919", "url": "https://glygen.org/publication/PubMed/23273919" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr64" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43583-1.45.45", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P43583-1.56.56", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43583-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43583-1.80.80", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 15 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RLYAADGRPHSPLRARSATP", "down_seq": "LQDQKLFNGMDSTSLLNERL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr66" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43583-1.48.48", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43583-1.56.56", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43583-1.78.78", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P43583-1.80.80", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LRARSATPTLQDQKLFNGMD", "down_seq": "TSLLNERLQHYTLDYVSDRA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser78" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43583-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43583-1.80.80", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ARSATPTLQDQKLFNGMDST", "down_seq": "LLNERLQHYTLDYVSDRAQH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser80" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43583-1.62.62", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P43583-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P43583-1.66.66", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43583-1.78.78", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43583-1.862.862", "start_pos": 862, "end_pos": 862, "uniprot_canonical_ac": "P43583-1", "length": 2143, "uniprot_id": "BLM10_YEAST", "protein_name": "Proteasome activator BLM10", "refseq_ac": "NP_116648", "refseq_name": "proteasome activator BLM10", "gene_name": "BLM10", "gene_names_uniprotkb": "BLM10; BLM3; YFL006W", "gene_names_refseq": "BLM10; YFL006W", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43583", "url": "https://www.uniprot.org/uniprotkb/P43583" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLLFHIKEQIKRGAGSVRST", "down_seq": "EIQQRDVKLVLYLTALNDVL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001887", "url": "https://www.yeastgenome.org/locus/S000001887" }, { "database": "iPTMnet", "id": "P43583", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43583" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser862" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "1663", "end_pos": "1664" }, { "start_pos": "2139", "end_pos": "2139" }, { "start_pos": "2140", "end_pos": "2140" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2141", "end_pos": "2143" }, { "start_pos": "2142", "end_pos": "2142" }, { "start_pos": "2143", "end_pos": "2143" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1006", "end_pos": "1006" }, { "start_pos": "1039", "end_pos": "1039" }, { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "862", "end_pos": "862" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Ypi1, a positive regulator of nuclear protein phosphatase type 1 activity in Saccharomyces cerevisiae.", "journal": "Molecular biology of the cell", "date": "2008-03", "authors": "Bharucha Jennifer P, Larson Jennifer R, Gao Lu, Daves Lisa K, Tatchell Kelly", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "reference": [ { "type": "PubMed", "id": "18172024", "url": "https://glygen.org/publication/PubMed/18172024" } ] } ], "crossref": [ { "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18172024", "url": "https://glygen.org/publication/PubMed/18172024", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "QLRATQDPPRSQEAMPTRHN", "down_seq": "RWEENVIDNENMNKKKTKIC", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "A", "comment": "Prevents interaction with GLC7.", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "PubMed", "id": "18172024", "url": "https://glygen.org/publication/PubMed/18172024" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P43587-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43587-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43587-1.53.53", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Molecular characterization of Ypi1, a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor.", "journal": "The Journal of biological chemistry", "date": "2003-11-28", "authors": "Garc\u00eda-Gimeno Maria Adelaida, Mu\u00f1oz Iv\u00e1n, Ari\u00f1o Joaqu\u00edn, Sanz Pascual", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "reference": [ { "type": "PubMed", "id": "14506263", "url": "https://glygen.org/publication/PubMed/14506263" } ] }, { "title": "Ypi1, a positive regulator of nuclear protein phosphatase type 1 activity in Saccharomyces cerevisiae.", "journal": "Molecular biology of the cell", "date": "2008-03", "authors": "Bharucha Jennifer P, Larson Jennifer R, Gao Lu, Daves Lisa K, Tatchell Kelly", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "reference": [ { "type": "PubMed", "id": "18172024", "url": "https://glygen.org/publication/PubMed/18172024" } ] } ], "crossref": [ { "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "14506263", "url": "https://glygen.org/publication/PubMed/14506263", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18172024", "url": "https://glygen.org/publication/PubMed/18172024", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "RATQDPPRSQEAMPTRHNVR", "down_seq": "EENVIDNENMNKKKTKICCI", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "Prevents interaction with GLC7 and reduces nuclear levels of GLC7 and SDS22.", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "PubMed", "id": "14506263", "url": "https://glygen.org/publication/PubMed/14506263" }, { "database": "PubMed", "id": "18172024", "url": "https://glygen.org/publication/PubMed/18172024" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43587-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43587-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43587-1.51.51", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proc. Natl. Acad. Sci. U.S.A.", "date": "2007", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FNERRQRRLERRHRKLEKKR", "down_seq": "YSPNAYEIQPDYSEYRRKQQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser131" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P43587-1.132.132", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43587-1.133.133", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43587-1.137.137", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43587-1.143.143", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 16 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NERRQRRLERRHRKLEKKRS", "down_seq": "SPNAYEIQPDYSEYRRKQQE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Tyr132" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P43587-1.131.131", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P43587-1.133.133", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P43587-1.137.137", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P43587-1.143.143", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.", "journal": "Proc. Natl. Acad. Sci. U.S.A.", "date": "2007", "authors": "Chi An, Huttenhower Curtis, Geer Lewis Y, Coon Joshua J, Syka John E P, Bai Dina L, Shabanowitz Jeffrey, Burke Daniel J, Troyanskaya Olga G, Hunt Donald F", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" } ] }, { "title": "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007-06-19", "authors": "Smolka Marcus B, Albuquerque Claudio P, Chen Sheng-hong, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.", "journal": "Proteomics", "date": "2009-10", "authors": "Gnad Florian, de Godoy Lyris M F, Cox J\u00fcrgen, Neuhauser Nadin, Ren Shubin, Olsen Jesper V, Mann Matthias", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" } ] }, { "title": "Global analysis of the yeast osmotic stress response by quantitative proteomics.", "journal": "Molecular bioSystems", "date": "2009-11", "authors": "Soufi Boumediene, Kelstrup Christian D, Stoehr Gabriele, Fr\u00f6hlich Florian, Walther Tobias C, Olsen Jesper V", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.", "journal": "Molecular biology of the cell", "date": "2010-10-01", "authors": "Soulard Alexandre, Cremonesi Alessio, Moes Suzette, Sch\u00fctz Fr\u00e9d\u00e9ric, Jen\u00f6 Paul, Hall Michael N", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" } ] }, { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Glucose intake hampers PKA-regulated HSP90 chaperone activity.", "journal": "eLife", "date": "2018-12-05", "authors": "Chen Yu-Chen, Jiang Pei-Heng, Chen Hsuan-Ming, Chen Chang-Han, Wang Yi-Ting, Chen Yu-Ju, Yu Chia-Jung, Teng Shu-Chun", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERRQRRLERRHRKLEKKRSY", "down_seq": "PNAYEIQPDYSEYRRKQQEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "PubMed", "id": "17287358", "url": "https://glygen.org/publication/PubMed/17287358" }, { "database": "PubMed", "id": "17563356", "url": "https://glygen.org/publication/PubMed/17563356" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19795423", "url": "https://glygen.org/publication/PubMed/19795423" }, { "database": "PubMed", "id": "19823750", "url": "https://glygen.org/publication/PubMed/19823750" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "PubMed", "id": "20702584", "url": "https://glygen.org/publication/PubMed/20702584" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "30516470", "url": "https://glygen.org/publication/PubMed/30516470" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser133" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43587-1.131.131", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P43587-1.132.132", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43587-1.137.137", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43587-1.143.143", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 16 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae.", "journal": "Journal of proteome research", "date": "2007-03", "authors": "Li Xue, Gerber Scott A, Rudner Adam D, Beausoleil Sean A, Haas Wilhelm, Vill\u00e9n Judit, Elias Joshua E, Gygi Steve P", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses.", "journal": "Journal of proteome research", "date": "2020-08-07", "authors": "MacGilvray Matthew E, Shishkova Evgenia, Place Michael, Wagner Ellen R, Coon Joshua J, Gasch Audrey P", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RRLERRHRKLEKKRSYSPNA", "down_seq": "EIQPDYSEYRRKQQEKKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "17330950", "url": "https://glygen.org/publication/PubMed/17330950" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "32597660", "url": "https://glygen.org/publication/PubMed/32597660" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Tyr137" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P43587-1.131.131", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P43587-1.132.132", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43587-1.133.133", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43587-1.143.143", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.", "journal": "Science signaling", "date": "2010-12-21", "authors": "Bodenmiller Bernd, Wanka Stefanie, Kraft Claudine, Urban J\u00f6rg, Campbell David, Pedrioli Patrick G, Gerrits Bertran, Picotti Paola, Lam Henry, Vitek Olga, Brusniak Mi-Youn, Roschitzki Bernd, Zhang Chao, Shokat Kevan M, Schlapbach Ralph, Colman-Lerner Alejandro, Nolan Garry P, Nesvizhskii Alexey I, Peter Matthias, Loewith Robbie, von Mering Christian, Aebersold Ruedi", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ] } ], "crossref": [ { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HRKLEKKRSYSPNAYEIQPD", "down_seq": "SEYRRKQQEKKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "21177495", "url": "https://glygen.org/publication/PubMed/21177495" } ], "site_lbl": "Tyr143" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P43587-1.131.131", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P43587-1.132.132", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P43587-1.133.133", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43587-1.137.137", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSGNQMAMGSEQQQTVG", "down_seq": "RTVSVEEVPAVLQLRATQDP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser18" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P43587-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43587-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P43587-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43587-1.35.35", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae.", "journal": "Molecular bioSystems", "date": "2012-03", "authors": "Pultz Dennis, Bennetzen Martin V, R\u00f8dk\u00e6r Steven Vestergaard, Zimmermann Christine, Enserink Jorrit M, Andersen Jens S, F\u00e6rgeman Nils J", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "", "down_seq": "VSVEEVPAVLQLRATQDPPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "22218487", "url": "https://glygen.org/publication/PubMed/22218487" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr20" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43587-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43587-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P43587-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P43587-1.35.35", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.", "journal": "Molecular & cellular proteomics : MCP", "date": "2005-03", "authors": "Gruhler Albrecht, Olsen Jesper V, Mohammed Shabaz, Mortensen Peter, Faergeman Nils J, Mann Matthias, Jensen Ole N", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" } ] }, { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Mol. Cell. Proteomics", "date": "2008", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution.", "journal": "Science (New York, N.Y.)", "date": "2009-09-25", "authors": "Holt Liam J, Tuch Brian B, Vill\u00e9n Judit, Johnson Alexander D, Gygi Steven P, Morgan David O", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" } ] }, { "title": "A global protein kinase and phosphatase interaction network in yeast.", "journal": "Science (New York, N.Y.)", "date": "2010-05-21", "authors": "Breitkreutz Ashton, Choi Hyungwon, Sharom Jeffrey R, Boucher Lorrie, Neduva Victor, Larsen Brett, Lin Zhen-Yuan, Breitkreutz Bobby-Joe, Stark Chris, Liu Guomin, Ahn Jessica, Dewar-Darch Danielle, Reguly Teresa, Tang Xiaojing, Almeida Ricardo, Qin Zhaohui Steve, Pawson Tony, Gingras Anne-Claude, Nesvizhskii Alexey I, Tyers Mike", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" } ] }, { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGNQMAMGSEQQQTVGSRTV", "down_seq": "VEEVPAVLQLRATQDPPRSQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" }, { "database": "PubMed", "id": "15665377", "url": "https://glygen.org/publication/PubMed/15665377" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "PubMed", "id": "19779198", "url": "https://glygen.org/publication/PubMed/19779198" }, { "database": "PubMed", "id": "20489023", "url": "https://glygen.org/publication/PubMed/20489023" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser22" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43587-1.2.2", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P43587-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P43587-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P43587-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43587-1.41.41", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels.", "journal": "BMC genomics", "date": "2010-12-02", "authors": "Helbig Andreas O, Rosati Sara, Pijnappel Pim W W M, van Breukelen Bas, Timmers Marc H T H, Mohammed Shabaz, Slijper Monique, Heck Albert J R", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "GNQMAMGSEQQQTVGSRTVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "21126336", "url": "https://glygen.org/publication/PubMed/21126336" }, { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P43587-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43587-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43587-1.22.22", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TVGSRTVSVEEVPAVLQLRA", "down_seq": "QDPPRSQEAMPTRHNVRWEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr35" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P43587-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P43587-1.20.20", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P43587-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43587-1.41.41", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P43587-1.51.51", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43587-1.53.53", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43587-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P43587-1", "length": 155, "uniprot_id": "YPI1_YEAST", "protein_name": "Type 1 phosphatases regulator YPI1", "refseq_ac": "NP_116658", "refseq_name": "type 1 protein phosphatase-activating protein YPI1", "gene_name": "YPI1", "gene_names_uniprotkb": "YPI1", "gene_names_refseq": "YPI1", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43587", "url": "https://www.uniprot.org/uniprotkb/P43587" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.", "journal": "Nature methods", "date": "2013-07", "authors": "Swaney Danielle L, Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J, Vill\u00e9n Judit", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSVEEVPAVLQLRATQDPPR", "down_seq": "QEAMPTRHNVRWEENVIDNE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001899", "url": "https://www.yeastgenome.org/locus/S000001899" }, { "database": "iPTMnet", "id": "P43587", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43587" }, { "database": "PubMed", "id": "23749301", "url": "https://glygen.org/publication/PubMed/23749301" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser41" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43587-1.22.22", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P43587-1.35.35", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P43587-1.51.51", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43587-1.53.53", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome.", "journal": "Science (New York, N.Y.)", "date": "2002-10-18", "authors": "Verma Rati, Aravind L, Oania Robert, McDonald W Hayes, Yates John R, Koonin Eugene V, Deshaies Raymond J", "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "reference": [ { "type": "PubMed", "id": "12183636", "url": "https://glygen.org/publication/PubMed/12183636" } ] } ], "crossref": [ { "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12183636", "url": "https://glygen.org/publication/PubMed/12183636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "AKMMDMLKQTGRDQMVVGWY", "down_seq": "SHPGFGCWLSSVDVNTQKSF", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Stabilizes ubiquitin pathway substrates; when associated wirh Ala-111.", "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" }, { "database": "PubMed", "id": "12183636", "url": "https://glygen.org/publication/PubMed/12183636" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P43588-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43588-1.128.128", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome.", "journal": "Science (New York, N.Y.)", "date": "2002-10-18", "authors": "Verma Rati, Aravind L, Oania Robert, McDonald W Hayes, Yates John R, Koonin Eugene V, Deshaies Raymond J", "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "reference": [ { "type": "PubMed", "id": "12183636", "url": "https://glygen.org/publication/PubMed/12183636" } ] } ], "crossref": [ { "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12183636", "url": "https://glygen.org/publication/PubMed/12183636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "MMDMLKQTGRDQMVVGWYHS", "down_seq": "PGFGCWLSSVDVNTQKSFEQ", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Stabilizes ubiquitin pathway substrates; when associated wirh Ala-109.", "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" }, { "database": "PubMed", "id": "12183636", "url": "https://glygen.org/publication/PubMed/12183636" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43588-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P43588-1.128.128", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YHSHPGFGCWLSSVDVNTQK", "down_seq": "FEQLNSRAVAVVVDPIQSVK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser128" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43588-1.109.109", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P43588-1.111.111", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P43588-1.134.134", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P43588-1.146.146", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FGCWLSSVDVNTQKSFEQLN", "down_seq": "RAVAVVVDPIQSVKGKVVID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser134" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P43588-1.128.128", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P43588-1.146.146", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKSFEQLNSRAVAVVVDPIQ", "down_seq": "VKGKVVIDAFRLIDTGALIN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser146" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P43588-1.128.128", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P43588-1.134.134", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MERLQRLMMNSKVG", "down_seq": "ADTGRDDTKETVYISSIALL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser15" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P43588-1.18.18", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MERLQRLMMNSKVGSAD", "down_seq": "GRDDTKETVYISSIALLKML", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr18" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P43588-1.15.15", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YHKTAKETKMLMNLHKEQWQ", "down_seq": "GLKMYDYEEKEESNLAATKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser223" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P43588-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P43588-1.243.243", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LHKEQWQSGLKMYDYEEKEE", "down_seq": "NLAATKSMVKIAEQYSKRIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser236" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P43588-1.223.223", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P43588-1.243.243", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGLKMYDYEEKEESNLAATK", "down_seq": "MVKIAEQYSKRIEEEKELTE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43588-1.223.223", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P43588-1.236.236", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43588-1.262.262", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "A multidimensional chromatography technology for in-depth phosphoproteome analysis.", "journal": "Molecular & cellular proteomics : MCP", "date": "2008-07", "authors": "Albuquerque Claudio P, Smolka Marcus B, Payne Samuel H, Bafna Vineet, Eng Jimmy, Zhou Huilin", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" } ] }, { "title": "Co- and post-translational modifications of the 26S proteasome in yeast.", "journal": "Proteomics", "date": "2010-08", "authors": "Kikuchi Julia, Iwafune Yuko, Akiyama Tomoko, Okayama Akiko, Nakamura Hiroki, Arakawa Noriaki, Kimura Yayoi, Hirano Hisashi", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" } ] }, { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSMVKIAEQYSKRIEEEKEL", "down_seq": "EEELKTRYVGRQDPKKHLSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "18407956", "url": "https://glygen.org/publication/PubMed/18407956" }, { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "PubMed", "id": "20486117", "url": "https://glygen.org/publication/PubMed/20486117" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Thr262" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43588-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P43588-1.281.281", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43588-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "P43588-1", "length": 306, "uniprot_id": "RPN11_YEAST", "protein_name": "Ubiquitin C-terminal hydrolase RPN11", "refseq_ac": "NP_116659", "refseq_name": "proteasome regulatory particle lid subunit RPN11", "gene_name": "RPN11", "gene_names_uniprotkb": "RPN11; MPR1", "gene_names_refseq": "MPR1; RPN11", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43588", "url": "https://www.uniprot.org/uniprotkb/P43588" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTEEELKTRYVGRQDPKKHL", "down_seq": "ETADETLENNIVSVLTAGVN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001900", "url": "https://www.yeastgenome.org/locus/S000001900" }, { "database": "iPTMnet", "id": "P43588", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43588" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser281" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "111", "end_pos": "111" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "281", "end_pos": "281" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P43588-1.262.262", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43594-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P43594-1", "length": 170, "uniprot_id": "MIC19_YEAST", "protein_name": "MICOS complex subunit MIC19", "refseq_ac": "NP_116666", "refseq_name": "Mic19p", "gene_name": "MIC19", "gene_names_uniprotkb": "MIC19; AIM13; MCS19", "gene_names_refseq": "AIM13; MCS19; MIC19", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43594", "url": "https://www.uniprot.org/uniprotkb/P43594" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QKLEKYGGAKGKSDKKTDNG", "down_seq": "ISIKAKLTECLLANKGKPLN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907" }, { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser136" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P43594-1.138.138", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43594-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P43594-1", "length": 170, "uniprot_id": "MIC19_YEAST", "protein_name": "MICOS complex subunit MIC19", "refseq_ac": "NP_116666", "refseq_name": "Mic19p", "gene_name": "MIC19", "gene_names_uniprotkb": "MIC19; AIM13; MCS19", "gene_names_refseq": "AIM13; MCS19; MIC19", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43594", "url": "https://www.uniprot.org/uniprotkb/P43594" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEKYGGAKGKSDKKTDNGSI", "down_seq": "IKAKLTECLLANKGKPLNCY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907" }, { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser138" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P43594-1.136.136", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43594-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "P43594-1", "length": 170, "uniprot_id": "MIC19_YEAST", "protein_name": "MICOS complex subunit MIC19", "refseq_ac": "NP_116666", "refseq_name": "Mic19p", "gene_name": "MIC19", "gene_names_uniprotkb": "MIC19; AIM13; MCS19", "gene_names_refseq": "AIM13; MCS19; MIC19", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43594", "url": "https://www.uniprot.org/uniprotkb/P43594" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DYVTKQNAEKFIEKKVSQRL", "down_seq": "NLEVETLKKFEDTLNNSLLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907" }, { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser61" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P43594-1.81.81", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43594-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P43594-1", "length": 170, "uniprot_id": "MIC19_YEAST", "protein_name": "MICOS complex subunit MIC19", "refseq_ac": "NP_116666", "refseq_name": "Mic19p", "gene_name": "MIC19", "gene_names_uniprotkb": "MIC19; AIM13; MCS19", "gene_names_refseq": "AIM13; MCS19; MIC19", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43594", "url": "https://www.uniprot.org/uniprotkb/P43594" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNLEVETLKKFEDTLNNSLL", "down_seq": "DDDKDAVDGISSSSLNNQIE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001907", "url": "https://www.yeastgenome.org/locus/S000001907" }, { "database": "iPTMnet", "id": "P43594", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43594" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser81" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P43594-1.61.61", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43596-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "P43596-1", "length": 787, "uniprot_id": "IOC3_YEAST", "protein_name": "ISWI one complex protein 3", "refseq_ac": "NP_116668", "refseq_name": "Ioc3p", "gene_name": "IOC3", "gene_names_uniprotkb": "IOC3", "gene_names_refseq": "IOC3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43596", "url": "https://www.uniprot.org/uniprotkb/P43596" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LYPGDPNGSAAGIVKGPEDT", "down_seq": "LLLYPDFMAIKDIVYCQDKM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909" }, { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser234" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "753", "end_pos": "753" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43596-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P43596-1", "length": 787, "uniprot_id": "IOC3_YEAST", "protein_name": "ISWI one complex protein 3", "refseq_ac": "NP_116668", "refseq_name": "Ioc3p", "gene_name": "IOC3", "gene_names_uniprotkb": "IOC3", "gene_names_refseq": "IOC3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43596", "url": "https://www.uniprot.org/uniprotkb/P43596" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] }, { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MD", "down_seq": "PSNSIQNLQQEAQGSSSAQL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909" }, { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser3" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "753", "end_pos": "753" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43596-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P43596-1", "length": 787, "uniprot_id": "IOC3_YEAST", "protein_name": "ISWI one complex protein 3", "refseq_ac": "NP_116668", "refseq_name": "Ioc3p", "gene_name": "IOC3", "gene_names_uniprotkb": "IOC3", "gene_names_refseq": "IOC3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43596", "url": "https://www.uniprot.org/uniprotkb/P43596" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLADHDHDRVSMAMPLQTDQ", "down_seq": "VSVSQSSDNLRRSRRVPKPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909" }, { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser42" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "753", "end_pos": "753" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43596-1.477.477", "start_pos": 477, "end_pos": 477, "uniprot_canonical_ac": "P43596-1", "length": 787, "uniprot_id": "IOC3_YEAST", "protein_name": "ISWI one complex protein 3", "refseq_ac": "NP_116668", "refseq_name": "Ioc3p", "gene_name": "IOC3", "gene_names_uniprotkb": "IOC3", "gene_names_refseq": "IOC3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43596", "url": "https://www.uniprot.org/uniprotkb/P43596" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "SUMO is a pervasive regulator of meiosis.", "journal": "eLife", "date": "2021-01-27", "authors": "Bhagwat Nikhil R, Owens Shannon N, Ito Masaru, Boinapalli Jay V, Poa Philip, Ditzel Alexander, Kopparapu Srujan, Mahalawat Meghan, Davies Owen Richard, Collins Sean R, Johnson Jeffrey R, Krogan Nevan J, Hunter Neil", "evidence": [ { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" } ], "reference": [ { "type": "PubMed", "id": "33502312", "url": "https://glygen.org/publication/PubMed/33502312" } ] } ], "crossref": [ { "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33502312", "url": "https://glygen.org/publication/PubMed/33502312", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IRSKKKHFVKQLKEGKKPDL", "down_seq": "RKLEILKEIKAELKNAVKSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909" }, { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" }, { "database": "PubMed", "id": "33502312", "url": "https://glygen.org/publication/PubMed/33502312" } ], "site_lbl": "Ser477" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "753", "end_pos": "753" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43596-1.753.753", "start_pos": 753, "end_pos": 753, "uniprot_canonical_ac": "P43596-1", "length": 787, "uniprot_id": "IOC3_YEAST", "protein_name": "ISWI one complex protein 3", "refseq_ac": "NP_116668", "refseq_name": "Ioc3p", "gene_name": "IOC3", "gene_names_uniprotkb": "IOC3", "gene_names_refseq": "IOC3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43596", "url": "https://www.uniprot.org/uniprotkb/P43596" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "In-depth and 3-dimensional exploration of the budding yeast phosphoproteome.", "journal": "EMBO reports", "date": "2021-02-03", "authors": "Lanz Michael C, Yugandhar Kumar, Gupta Shagun, Sanford Ethan J, Fa\u00e7a Vitor M, Vega Stephanie, Joiner Aaron M N, Fromme J Christopher, Yu Haiyuan, Smolka Marcus B", "evidence": [ { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" } ], "reference": [ { "type": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ] } ], "crossref": [ { "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKRQLRRIQRQTVNYNTEYD", "down_seq": "EEYVDDEEDDEADIYDDNDN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001909", "url": "https://www.yeastgenome.org/locus/S000001909" }, { "database": "iPTMnet", "id": "P43596", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43596" }, { "database": "PubMed", "id": "33491328", "url": "https://glygen.org/publication/PubMed/33491328" } ], "site_lbl": "Ser753" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "753", "end_pos": "753" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43609-1.347.351", "start_pos": 347, "end_pos": 351, "uniprot_canonical_ac": "P43609-1", "length": 557, "uniprot_id": "RSC8_YEAST", "protein_name": "Chromatin structure-remodeling complex protein RSC8", "refseq_ac": "NP_116695", "refseq_name": "Rsc8p", "gene_name": "RSC8", "gene_names_uniprotkb": "RSC8; SWH3", "gene_names_refseq": "RSC8; SWH3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43609", "url": "https://www.uniprot.org/uniprotkb/P43609" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes.", "journal": "Molecular cell", "date": "2002-10", "authors": "Boyer Laurie A, Langer Michael R, Crowley Kimberly A, Tan Song, Denu John M, Peterson Craig L", "evidence": [ { "database": "UniProtKB", "id": "P43609", "url": "https://www.uniprot.org/uniprotkb/P43609" } ], "reference": [ { "type": "PubMed", "id": "12419236", "url": "https://glygen.org/publication/PubMed/12419236" } ] } ], "crossref": [ { "id": "P43609", "url": "https://www.uniprot.org/uniprotkb/P43609", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12419236", "url": "https://glygen.org/publication/PubMed/12419236", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "VEDCI", "start_aa": "V", "up_seq": "IEMYEDQWEKIADHVGGHKR", "down_seq": "EKFLSLPIEDNYIREVVGST", "mutagenesis": [ { "sequence_org": "VEDCI", "sequence_mut": "", "comment": "Loss of function.", "evidence": [ { "database": "UniProtKB", "id": "P43609", "url": "https://www.uniprot.org/uniprotkb/P43609" }, { "database": "PubMed", "id": "12419236", "url": "https://glygen.org/publication/PubMed/12419236" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "347", "end_pos": "351" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "556", "end_pos": "556" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P43609-1.370.370", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P43609-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P43609-1", "length": 557, "uniprot_id": "RSC8_YEAST", "protein_name": "Chromatin structure-remodeling complex protein RSC8", "refseq_ac": "NP_116695", "refseq_name": "Rsc8p", "gene_name": "RSC8", "gene_names_uniprotkb": "RSC8; SWH3", "gene_names_refseq": "RSC8; SWH3", "species": [ { "name": "Saccharomyces cerevisiae S288C", "taxid": 559292, "evidence": [ { "database": "UniProtKB", "id": "P43609", "url": "https://www.uniprot.org/uniprotkb/P43609" } ], "common_name": "Baker's yeast", "glygen_name": "Yeast", "reference_species": "Saccharomyces cerevisiae S288C [559292]" } ], "publication": [ { "title": "Cross-compartment signal propagation in the mitotic exit network.", "journal": "eLife", "date": "2021-01-22", "authors": "Zhou Xiaoxue, Li Wenxue, Liu Yansheng, Amon Angelika", "evidence": [ { "database": "iPTMnet", "id": "P43609", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43609" } ], "reference": [ { "type": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ] } ], "crossref": [ { "id": "S000001933", "url": "https://www.yeastgenome.org/locus/S000001933", "database": "SGD", "categories": [ "Organism-specific" ] }, { "id": "P43609", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43609", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPYEYLTITAVRRNVAMDVA", "down_seq": "IVKIHAFLEKWGLINYQIDP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "SGD", "id": "S000001933", "url": "https://www.yeastgenome.org/locus/S000001933" }, { "database": "iPTMnet", "id": "P43609", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P43609" }, { "database": "PubMed", "id": "33481703", "url": "https://glygen.org/publication/PubMed/33481703" } ], "site_lbl": "Ser152" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "347", "end_pos": "351" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "556", "end_pos": "556" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] } ]